Model_id	Action	ARO_name	ARO_category	Changes To	Summary
1718	UPDATE	DIM-1	 carbapenem;  antibiotic inactivation;  cephalosporin;  DIM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1867	UPDATE	CTX-M-116	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2031	UPDATE	OXA-173	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1200	UPDATE	msrA	 quinupristin;  macrolide antibiotic;  streptogramin B antibiotic;  msr-type ABC-F protein;  antibiotic target protection;  streptogramin antibiotic;  erythromycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1866	UPDATE	KPC-7	 antibiotic inactivation;  penam;  carbapenem;  cephalosporin;  monobactam;  KPC beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1020	UPDATE	OXA-241	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4026	UPDATE	PDC-461	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4027	UPDATE	PDC-19a	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4024	UPDATE	PDC-19b	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4025	UPDATE	PDC-380	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4022	UPDATE	PDC-352	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4023	UPDATE	PDC-464	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4020	UPDATE	PDC-337	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4021	UPDATE	PDC-212	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
643	UPDATE	OXY-2-5	 penam;  OXY beta-lactamase;  cephalosporin;  antibiotic inactivation;  monobactam; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4028	UPDATE	PDC-272	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4029	UPDATE	PDC-255	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3383	UPDATE	MCR-9.1	 peptide antibiotic;  MCR phosphoethanolamine transferase;  antibiotic target alteration;  colistin B;  colistin A; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
981	UPDATE	OXA-86	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
344	UPDATE	SHV-188	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  SHV beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
345	UPDATE	bcrA	 peptide antibiotic;  ATP-binding cassette (ABC) antibiotic efflux pump;  efflux pump complex or subunit conferring antibiotic resistance;  antibiotic efflux;  bacitracin B;  bacitracin F;  bacitracin A;  bacitracin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
346	UPDATE	QnrB23	 sparfloxacin;  norfloxacin;  quinolone resistance protein (qnr);  gatifloxacin;  levofloxacin;  antibiotic target protection;  ciprofloxacin;  fluoroquinolone antibiotic;  nalidixic acid;  moxifloxacin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
347	UPDATE	SFH-1	 SFH beta-lactamase;  carbapenem;  antibiotic inactivation; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
340	UPDATE	CMY-51	 antibiotic inactivation;  CMY beta-lactamase;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
341	UPDATE	IMP-1	 penam;  antibiotic inactivation;  penem;  carbapenem;  cephalosporin;  IMP beta-lactamase;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
342	UPDATE	smeS	 penam;  antibiotic efflux;  resistance-nodulation-cell division (RND) antibiotic efflux pump;  protein(s) and two-component regulatory system modulating antibiotic efflux;  efflux pump complex or subunit conferring antibiotic resistance;  cephalosporin;  cephamycin;  aminoglycoside antibiotic; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
343	UPDATE	OXA-31	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3997	UPDATE	TEM-234	 penam;  antibiotic inactivation;  penem;  cephalosporin;  monobactam;  ampicillin;  TEM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3996	UPDATE	TEM-233	 penam;  antibiotic inactivation;  penem;  cephalosporin;  monobactam;  ampicillin;  TEM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3995	UPDATE	TEM-232	 penam;  antibiotic inactivation;  penem;  cephalosporin;  monobactam;  ampicillin;  TEM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3994	UPDATE	TEM-231	 penam;  antibiotic inactivation;  penem;  cephalosporin;  monobactam;  ampicillin;  TEM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
348	UPDATE	OXY-3-1	 penam;  OXY beta-lactamase;  cephalosporin;  antibiotic inactivation;  monobactam; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3992	UPDATE	TEM-229	 penam;  antibiotic inactivation;  penem;  cephalosporin;  monobactam;  ampicillin;  TEM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3991	UPDATE	TEM-228	 penam;  antibiotic inactivation;  penem;  cephalosporin;  monobactam;  ampicillin;  TEM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3990	UPDATE	TEM-227	 penam;  antibiotic inactivation;  penem;  cephalosporin;  monobactam;  ampicillin;  TEM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4930	UPDATE	OXA-604	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
595	UPDATE	SHV-75	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  SHV beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4844	UPDATE	OXA-509	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
965	UPDATE	OXA-333	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1343	UPDATE	OXA-166	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
966	UPDATE	vanS gene in vanC cluster	 glycopeptide antibiotic;  vanS;  antibiotic target alteration;  vancomycin;  glycopeptide resistance gene cluster; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with vancomycin
UPDATED category_aro_cvterm_id with 35947
UPDATED category_aro_accession with 0000028
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3573	UPDATE	CIA-4	 carbapenem;  antibiotic inactivation;  cephalosporin;  CIA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
967	UPDATE	AAC(6')-Isa	 AAC(6');  antibiotic inactivation;  aminoglycoside antibiotic; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2132	UPDATE	Mycobacterium tuberculosis 16S rRNA mutation conferring resistance to kanamycin	 kanamycin A;  antibiotic target alteration;  aminoglycoside antibiotic;  16s rRNA with mutation conferring resistance to aminoglycoside antibiotics; 	model_description; model_param	"UPDATED model_description with Ribosomal RNA (rRNA) Gene Variant Models (RVM) are similar to Protein Variant Models (PVM), i.e. detect  sequences based on their similarity to a curated reference sequence and secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles, except RVMs are designed to detect AMR acquired via mutation of genes encoding ribosomal RNAs (rRNA). RVMs include a rRNA reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTN bit-score above the curated BLASTN cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTN bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
UPDATED param_description with The BLASTN bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
"
1296	UPDATE	OKP-B-12	 penam;  antibiotic inactivation;  OKP beta-lactamase;  cephalosporin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
960	UPDATE	TEM-137	 penam;  antibiotic inactivation;  penem;  cephalosporin;  monobactam;  ampicillin;  TEM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
961	UPDATE	SHV-93	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  SHV beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4732	UPDATE	KPC-73	 antibiotic inactivation;  penam;  carbapenem;  cephalosporin;  monobactam;  KPC beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4733	UPDATE	KPC-74	 antibiotic inactivation;  penam;  carbapenem;  cephalosporin;  monobactam;  KPC beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4730	UPDATE	KPC-71	 antibiotic inactivation;  penam;  carbapenem;  cephalosporin;  monobactam;  KPC beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4731	UPDATE	KPC-72	 antibiotic inactivation;  penam;  carbapenem;  cephalosporin;  monobactam;  KPC beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4736	UPDATE	KPC-77	 antibiotic inactivation;  penam;  carbapenem;  cephalosporin;  monobactam;  KPC beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4737	UPDATE	KPC-78	 antibiotic inactivation;  penam;  carbapenem;  cephalosporin;  monobactam;  KPC beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4734	UPDATE	KPC-75	 antibiotic inactivation;  penam;  carbapenem;  cephalosporin;  monobactam;  KPC beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4735	UPDATE	KPC-76	 antibiotic inactivation;  penam;  carbapenem;  cephalosporin;  monobactam;  KPC beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2317	UPDATE	mgrB	 resistance by absence; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Knockout Models (PKM) reflect resistance by the absence of a gene product, most often deletion of a gene involved in antibiotic import, such as Vibrio cholerae OmpT. Like Protein Homolog Models (PHMs), PKMs include a reference sequence and a bitscore cut-off for detection using BLASTP but instead are designed to only report lack of detection under Perfect or Strict criteria. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff. This model type is still under development and not currently supported by the Resistance Gene Identifier (RGI) software.
DELETED 36001
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2314	UPDATE	Acinetobacter baumannii gyrA conferring resistance to fluoroquinolones	 grepafloxacin;  trovafloxacin;  ofloxacin;  norfloxacin;  nalidixic acid;  lomefloxacin;  gatifloxacin;  fluoroquinolone resistant gyrA;  levofloxacin;  sparfloxacin;  antibiotic target alteration;  enoxacin;  ciprofloxacin;  pefloxacin;  fluoroquinolone antibiotic;  moxifloxacin; 	model_description; model_param	"UPDATED model_description with Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
"
2315	UPDATE	Acinetobacter baumannii parC conferring resistance to fluoroquinolones	 grepafloxacin;  trovafloxacin;  ofloxacin;  norfloxacin;  nalidixic acid;  lomefloxacin;  gatifloxacin;  sparfloxacin;  levofloxacin;  fluoroquinolone resistant parC;  antibiotic target alteration;  enoxacin;  ciprofloxacin;  pefloxacin;  fluoroquinolone antibiotic;  moxifloxacin; 	model_description; model_param	"UPDATED model_description with Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
"
2310	UPDATE	Streptomyces cinnamoneus EF-Tu mutants conferring resistance to elfamycin	 antibiotic target alteration;  elfamycin antibiotic;  kirromycin;  elfamycin resistant EF-Tu; 	model_description; model_param	"UPDATED model_description with Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
"
4831	UPDATE	OXA-493	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2184	UPDATE	glycopeptide resistance gene cluster VanC	 glycopeptide antibiotic;  glycopeptide resistance gene cluster;  antibiotic target alteration;  vancomycin; 	model_description; ARO_category; model_param	"UPDATED model_description with Gene Cluster Meta-Models (PKM) are used to curate spatial clusters of individual genes within operons, such as for glycopeptide resistance gene clusters. The individual genes will have their own individual detection models (e.g. PHM, PVM, POM, etc.) while the PKM checks to see if all the component genes of the cluster have a Strict or Perfect hit and are ordered correctly within an operon. PKMs are encoded using the gene order parameter. This model type is still under development and not currently supported by the Resistance Gene Identifier (RGI) software.
UPDATED category_aro_name with vancomycin
UPDATED category_aro_cvterm_id with 35947
UPDATED category_aro_accession with 0000028
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.
UPDATED param_description with Spatial clusters of genes are encoded using the gene order parameter: [gene type]:[cvterm_id],[gene type]:[cvterm_id], etc. The gene type designations are: R = regulatory, C = core, A = accessory.
"
298	UPDATE	vanY gene in vanG cluster	 glycopeptide antibiotic;  glycopeptide resistance gene cluster;  antibiotic target alteration;  vancomycin;  vanY; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with vancomycin
UPDATED category_aro_cvterm_id with 35947
UPDATED category_aro_accession with 0000028
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.
UPDATED param_value with 50
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
299	UPDATE	CepS	 CepS beta-lactamase;  antibiotic inactivation;  cephalosporin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
296	UPDATE	VIM-23	 penam;  antibiotic inactivation;  penem;  carbapenem;  cephalosporin;  cephamycin;  VIM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
297	UPDATE	CMY-98	 antibiotic inactivation;  CMY beta-lactamase;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
294	UPDATE	CfxA4	 antibiotic inactivation;  cephamycin;  CfxA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
295	UPDATE	OXA-145	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
292	UPDATE	TEM-17	 penam;  antibiotic inactivation;  penem;  cephalosporin;  monobactam;  ampicillin;  TEM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
293	UPDATE	SHV-180	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  SHV beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
290	UPDATE	vatD	 dalfopristin;  antibiotic inactivation;  streptogramin vat acetyltransferase;  virginiamycin M1;  madumycin II;  griseoviridin;  streptogramin A antibiotic;  streptogramin antibiotic; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
291	UPDATE	APH(3')-Ia	 antibiotic inactivation;  aminoglycoside antibiotic;  paromomycin;  kanamycin A;  APH(3');  lividomycin B;  ribostamycin;  G418;  neomycin;  lividomycin A; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3773	UPDATE	CTX-M-161	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3772	UPDATE	FLC-1	 FRI beta-lactamase;  penam;  antibiotic inactivation; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3771	UPDATE	FRI-9	 FRI beta-lactamase;  penam;  antibiotic inactivation; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3770	UPDATE	FRI-8	 FRI beta-lactamase;  penam;  antibiotic inactivation; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3777	UPDATE	CTX-M-165	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3776	UPDATE	CTX-M-164	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3775	UPDATE	CTX-M-163	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3774	UPDATE	CTX-M-162	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4835	UPDATE	OXA-500	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3779	UPDATE	Yrc-1	 penam;  antibiotic inactivation;  cephalosporin;  YRC Beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3778	UPDATE	CTX-M-166	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2782	UPDATE	Vibrio cholerae OmpU	 peptide antibiotic;  BPI;  General Bacterial Porin with reduced permeability to peptide antibiotics;  reduced permeability to antibiotic; 	model_description	"UPDATED model_description with Protein Knockout Models (PKM) reflect resistance by the absence of a gene product, most often deletion of a gene involved in antibiotic import, such as Vibrio cholerae OmpT. Like Protein Homolog Models (PHMs), PKMs include a reference sequence and a bitscore cut-off for detection using BLASTP but instead are designed to only report lack of detection under Perfect or Strict criteria. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff. This model type is still under development and not currently supported by the Resistance Gene Identifier (RGI) software.
"
4834	UPDATE	OXA-498	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
270	UPDATE	LEN-20	 penam;  LEN beta-lactamase;  antibiotic inactivation;  penem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
271	UPDATE	CMY-4	 antibiotic inactivation;  CMY beta-lactamase;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
272	UPDATE	QnrB36	 sparfloxacin;  norfloxacin;  quinolone resistance protein (qnr);  gatifloxacin;  levofloxacin;  antibiotic target protection;  ciprofloxacin;  fluoroquinolone antibiotic;  nalidixic acid;  moxifloxacin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
273	UPDATE	VEB-7	 antibiotic inactivation;  monobactam;  cephalosporin;  VEB beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
274	UPDATE	OXA-174	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
275	UPDATE	OKP-B-2	 penam;  antibiotic inactivation;  OKP beta-lactamase;  cephalosporin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
276	UPDATE	tetR	 antibiotic efflux;  major facilitator superfamily (MFS) antibiotic efflux pump;  protein(s) and two-component regulatory system modulating antibiotic efflux;  efflux pump complex or subunit conferring antibiotic resistance;  tetracycline antibiotic;  antibiotic target alteration;  tetracycline; 	model_description; model_param	"UPDATED model_description with Protein Overexpression Models (POM) are similar to Protein Variant Models (PVM) in that they include a protein reference sequence, a curated BLASTP bitscore cut-off, and mapped resistance variants. Whereas PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, reporting only those with curated mutations conferring AMR, POMs are restricted to regulatory proteins and report both wild-type sequences and/or sequences with mutations leading to overexpression of efflux complexes. The former lead to efflux of antibiotics at basal levels, while the latter can confer clinical resistance. POMs include a protein reference sequence (often from wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Perfect RGI match is 100% identical to the wild-type reference protein sequence along its entire length, a Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value may or may not contain at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off may or may not contain at least one curated mutation from amongst the mapped resistance variants.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
"
277	UPDATE	TEM-91	 penam;  antibiotic inactivation;  penem;  cephalosporin;  monobactam;  ampicillin;  TEM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
278	UPDATE	imiS	 carbapenem;  CphA beta-lactamase;  antibiotic inactivation; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
279	UPDATE	CTX-M-107	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4836	UPDATE	OXA-501	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4659	UPDATE	GOB-46	 carbapenem;  penam;  GOB beta-lactamase;  antibiotic inactivation;  cephalosporin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4658	UPDATE	GOB-45	 carbapenem;  penam;  GOB beta-lactamase;  antibiotic inactivation;  cephalosporin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
581	UPDATE	QnrB19	 sparfloxacin;  norfloxacin;  quinolone resistance protein (qnr);  gatifloxacin;  levofloxacin;  antibiotic target protection;  ciprofloxacin;  fluoroquinolone antibiotic;  nalidixic acid;  moxifloxacin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2268	UPDATE	eatAv	 Miscellaneous ABC-F subfamily ATP-binding cassette ribosomal protection proteins;  pleuromutilin antibiotic;  antibiotic target protection;  pleuromutilin; 	model_description; model_param	"UPDATED model_description with Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
"
46	UPDATE	CMY-114	 antibiotic inactivation;  CMY beta-lactamase;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1132	UPDATE	OXA-88	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2262	UPDATE	mefC	 efflux pump complex or subunit conferring antibiotic resistance;  major facilitator superfamily (MFS) antibiotic efflux pump;  macrolide antibiotic;  antibiotic efflux; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2263	UPDATE	optrA	 tedizolid;  antibiotic target protection;  Miscellaneous ABC-F subfamily ATP-binding cassette ribosomal protection proteins;  linezolid;  florfenicol;  oxazolidinone antibiotic;  phenicol antibiotic;  chloramphenicol; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2260	UPDATE	vatF	 dalfopristin;  antibiotic inactivation;  streptogramin vat acetyltransferase;  virginiamycin M1;  madumycin II;  griseoviridin;  streptogramin A antibiotic;  streptogramin antibiotic; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2261	UPDATE	lnuE	 antibiotic inactivation;  lincosamide nucleotidyltransferase (LNU);  lincomycin;  lincosamide antibiotic; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with lincomycin
UPDATED category_aro_cvterm_id with 35964
UPDATED category_aro_accession with 0000046
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Lincomycin is a lincosamide antibiotic that comes from the actinomyces Streptomyces lincolnensis. It binds to the 23s portion of the 50S subunit of bacterial ribosomes and inhibit early elongation of peptide chain by inhibiting transpeptidase reaction.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2267	UPDATE	Escherichia coli nfsA mutations conferring resistance to nitrofurantoin	 antibiotic target alteration;  nitrofuran antibiotic;  nitrofurantoin;  antibiotic resistant nfsA; 	model_description; model_param	"UPDATED model_description with Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
UPDATED param_description with A subtype of the deletion mutation detection model parameter used when a set of deletion mutations are reported in a peptide sequence format, encoded as [-][AAs][position range], for example -K527 or -QN517-518.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A subtype of the deletion mutation detection model parameter used when a set of deletion mutations are reported in a nucleotide sequence format, encoded as [-]nt[position]:[nucleotides], for example -nt25:T.
UPDATED param_description with A nucleotide substitution resulting in a change from an amino acid codon to a STOP codon, encoded as [wild type amino acid][position][STOP], for example Q42STOP.
"
2264	UPDATE	oleC	 efflux pump complex or subunit conferring antibiotic resistance;  ATP-binding cassette (ABC) antibiotic efflux pump;  macrolide antibiotic;  oleandomycin;  antibiotic efflux; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2265	UPDATE	salA	 retapamulin;  sal-type ABC-F protein;  virginiamycin M1;  pleuromutilin antibiotic;  tiamulin;  streptogramin A antibiotic;  lincomycin;  antibiotic target protection;  streptogramin antibiotic;  clindamycin;  lincosamide antibiotic; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2346	UPDATE	ADC-16	 antibiotic inactivation;  cephalosporin;  ADC beta-lactamase without carbapenemase activity; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
963	UPDATE	CMY-69	 antibiotic inactivation;  CMY beta-lactamase;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2445	UPDATE	Erm(44)v	 Erm 23S ribosomal RNA methyltransferase;  erythromycin;  macrolide antibiotic;  antibiotic target alteration;  streptogramin antibiotic;  clindamycin;  lincosamide antibiotic; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with clindamycin
UPDATED category_aro_cvterm_id with 35983
UPDATED category_aro_accession with 0000066
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Clindamycin is a lincosamide antibiotic that blocks A-site aminoacyl-tRNA binding. It is usually used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria.
UPDATED category_aro_name with erythromycin
UPDATED category_aro_cvterm_id with 35925
UPDATED category_aro_accession with 0000006
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure/function processes critical for life or replication are inhibited.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4535	UPDATE	CTX-M-206	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
47	UPDATE	OXA-60	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
108	UPDATE	PDC-8	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
109	UPDATE	ErmE	 streptogramin A antibiotic;  antibiotic target alteration;  virginiamycin S2;  vernamycin C;  pristinamycin IC;  patricin B;  patricin A;  oleandomycin;  ostreogrycin B3;  macrolide antibiotic;  telithromycin;  tylosin;  lincosamide antibiotic;  dirithromycin;  clarithromycin;  clindamycin;  dalfopristin;  pristinamycin IB;  quinupristin;  pristinamycin IA;  Erm 23S ribosomal RNA methyltransferase;  virginiamycin M1;  madumycin II;  griseoviridin;  streptogramin B antibiotic;  lincomycin;  streptogramin antibiotic;  roxithromycin;  spiramycin;  azithromycin;  erythromycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
102	UPDATE	TLA-2	 antibiotic inactivation;  monobactam;  fluoroquinolone antibiotic;  cephalosporin;  TLA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
103	UPDATE	SHV-12	 penam;  antibiotic inactivation;  cephalosporin;  carbapenem;  ceftazidime;  cefalotin;  ceftriaxone;  SHV beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
100	UPDATE	Mycobacterium tuberculosis ethA with mutation conferring resistance to ethionamide	 thioamide antibiotic;  antibiotic target alteration;  ethionamide;  ethionamide resistant ethA; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Ethionamide is a second-line antitubercular agent that inhibits mycolic acid synthesis.
UPDATED category_aro_name with thioamide antibiotic
UPDATED category_aro_cvterm_id with 45738
UPDATED category_aro_accession with 3007156
UPDATED category_aro_class_name with Drug Class
UPDATED category_aro_description with A group of antibiotics possessing the thioamide functional group.
UPDATED param_description with A subtype of the insertion mutation detection model parameter used when a set of insertion mutations are reported in a nucleotide sequence format, encoded as [+]nt[position]:[nucleotides], for example +nt391:GG. Such mutations may be of variable length, possibly causing a frameshift but not causing premature termination or a functional knockout.
UPDATED param_description with A SNP in the promoter region of a gene which alters transcription of that gene, encoded as nt[wild-type][-][position][mutation], for example ntT-11C. This is a pilot parameter in need of further documentation.
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A subtype of the deletion mutation detection model parameter used when a set of deletion mutations are reported in a nucleotide sequence format, encoded as [-]nt[position]:[nucleotides], for example -nt25:T.
"
101	UPDATE	TEM-109	 penam;  antibiotic inactivation;  penem;  cephalosporin;  monobactam;  ampicillin;  TEM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
106	UPDATE	catB9	 antibiotic inactivation;  thiamphenicol;  chloramphenicol acetyltransferase (CAT);  azidamfenicol;  phenicol antibiotic;  chloramphenicol; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
107	UPDATE	TEM-43	 penam;  antibiotic inactivation;  penem;  cephalosporin;  monobactam;  ampicillin;  TEM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
104	UPDATE	OXA-61	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
105	UPDATE	CARB-4	 penam;  antibiotic inactivation;  CARB beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2046	UPDATE	tet(33)	 tetracycline antibiotic;  efflux pump complex or subunit conferring antibiotic resistance;  major facilitator superfamily (MFS) antibiotic efflux pump;  tetracycline;  antibiotic efflux; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2047	UPDATE	OXA-322	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2044	UPDATE	QnrB31	 sparfloxacin;  norfloxacin;  quinolone resistance protein (qnr);  gatifloxacin;  levofloxacin;  antibiotic target protection;  ciprofloxacin;  fluoroquinolone antibiotic;  nalidixic acid;  moxifloxacin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2045	UPDATE	OXY-2-3	 penam;  OXY beta-lactamase;  cephalosporin;  antibiotic inactivation;  monobactam; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2042	UPDATE	IND-8	 carbapenem;  antibiotic inactivation;  IND beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2043	UPDATE	aadA8	 antibiotic inactivation;  aminoglycoside antibiotic;  ANT(3'');  streptomycin;  spectinomycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2040	UPDATE	TEM-60	 penam;  antibiotic inactivation;  penem;  cephalosporin;  monobactam;  ampicillin;  TEM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2041	UPDATE	OXA-424	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4819	UPDATE	OXA-114t	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4818	UPDATE	OXA-114s	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1297	UPDATE	CTX-M-80	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2048	UPDATE	OXA-57	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2049	UPDATE	QnrB72	 sparfloxacin;  norfloxacin;  quinolone resistance protein (qnr);  gatifloxacin;  levofloxacin;  antibiotic target protection;  ciprofloxacin;  fluoroquinolone antibiotic;  nalidixic acid;  moxifloxacin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1189	UPDATE	vatB	 dalfopristin;  antibiotic inactivation;  streptogramin vat acetyltransferase;  virginiamycin M1;  madumycin II;  griseoviridin;  streptogramin A antibiotic;  streptogramin antibiotic; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4144	UPDATE	ACT-53	 antibiotic inactivation;  carbapenem;  penam;  ACT beta-lactamase;  cephalosporin;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4011	UPDATE	PDC-384	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
449	UPDATE	SHV-133	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  SHV beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1364	UPDATE	CMY-101	 antibiotic inactivation;  CMY beta-lactamase;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1060	UPDATE	SHV-103	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  SHV beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4849	UPDATE	OXA-514	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3519	UPDATE	OXA-450	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3518	UPDATE	OXA-449	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5298	UPDATE	PDC-16	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3513	UPDATE	OXA-443	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3512	UPDATE	OXA-442	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3511	UPDATE	OXA-441	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3510	UPDATE	OXA-440	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3517	UPDATE	OXA-448	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3516	UPDATE	OXA-447	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3515	UPDATE	OXA-446	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3514	UPDATE	OXA-444	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1420	UPDATE	aadA5	 antibiotic inactivation;  aminoglycoside antibiotic;  ANT(3'');  streptomycin;  spectinomycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2688	UPDATE	ArmR	 sulfonamide antibiotic;  penem;  panipenem;  tetracycline antibiotic;  clavulanic acid;  meropenem;  antibiotic efflux;  resistance-nodulation-cell division (RND) antibiotic efflux pump;  aztreonam;  trimethoprim;  aminocoumarin antibiotic;  cephalosporin;  macrolide antibiotic;  carbapenem;  ceftazidime;  ciprofloxacin;  cephamycin;  ceftriaxone;  amoxicillin-clavulanic acid;  colistin B;  protein(s) and two-component regulatory system modulating antibiotic efflux;  colistin A;  peptide antibiotic;  diaminopyrimidine antibiotic;  ampicillin;  amoxicillin;  penam;  sulfamethoxazole;  novobiocin;  efflux pump complex or subunit conferring antibiotic resistance;  trimethoprim-sulfamethoxazole;  tetracycline;  monobactam;  fluoroquinolone antibiotic;  erythromycin;  phenicol antibiotic;  azithromycin;  chloramphenicol; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2689	UPDATE	Staphylococcus aureus 23S rRNA with mutation conferring resistance to linezolid	 23S rRNA with mutation conferring resistance to linezolid antibiotics;  pleuromutilin antibiotic;  macrolide antibiotic;  linezolid;  streptogramin antibiotic;  glycopeptide antibiotic;  oxazolidinone antibiotic;  antibiotic target alteration;  phenicol antibiotic;  lincosamide antibiotic; 	model_description; model_param	"UPDATED model_description with Ribosomal RNA (rRNA) Gene Variant Models (RVM) are similar to Protein Variant Models (PVM), i.e. detect  sequences based on their similarity to a curated reference sequence and secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles, except RVMs are designed to detect AMR acquired via mutation of genes encoding ribosomal RNAs (rRNA). RVMs include a rRNA reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTN bit-score above the curated BLASTN cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTN bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
UPDATED param_description with The BLASTN bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
"
2685	UPDATE	Pseudomonas aeruginosa CpxR	 sulfonamide antibiotic;  penem;  panipenem;  tetracycline antibiotic;  clavulanic acid;  meropenem;  antibiotic efflux;  resistance-nodulation-cell division (RND) antibiotic efflux pump;  aztreonam;  trimethoprim;  aminocoumarin antibiotic;  cephalosporin;  macrolide antibiotic;  carbapenem;  ceftazidime;  ciprofloxacin;  cephamycin;  ceftriaxone;  amoxicillin-clavulanic acid;  colistin B;  protein(s) and two-component regulatory system modulating antibiotic efflux;  colistin A;  peptide antibiotic;  diaminopyrimidine antibiotic;  ampicillin;  amoxicillin;  penam;  aminoglycoside antibiotic;  sulfamethoxazole;  novobiocin;  efflux pump complex or subunit conferring antibiotic resistance;  trimethoprim-sulfamethoxazole;  tetracycline;  monobactam;  fluoroquinolone antibiotic;  erythromycin;  phenicol antibiotic;  azithromycin;  chloramphenicol; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2686	UPDATE	MexAB-OprM with CpxR regulator conferring resistance to ciprofloxacin, ceftazidime, and aztreonam	 sulfonamide antibiotic;  penem;  panipenem;  tetracycline antibiotic;  clavulanic acid;  meropenem;  antibiotic efflux;  resistance-nodulation-cell division (RND) antibiotic efflux pump;  aztreonam;  trimethoprim;  aminocoumarin antibiotic;  cephalosporin;  macrolide antibiotic;  carbapenem;  ceftazidime;  ciprofloxacin;  cephamycin;  ceftriaxone;  amoxicillin-clavulanic acid;  colistin B;  colistin A;  peptide antibiotic;  diaminopyrimidine antibiotic;  ampicillin;  amoxicillin;  penam;  sulfamethoxazole;  novobiocin;  efflux pump complex or subunit conferring antibiotic resistance;  trimethoprim-sulfamethoxazole;  tetracycline;  monobactam;  fluoroquinolone antibiotic;  erythromycin;  phenicol antibiotic;  azithromycin;  chloramphenicol; 	model_description; model_param	"UPDATED model_description with Efflux Pump System Meta-Models (EPS) are dedicated to efflux complexes and their regulators, such as AcrAB-TolC. Using the efflux pump components parameter, this model type simply includes a list of detection models for each component of the complex. This model type is still under development and not currently supported by the Resistance Gene Identifier (RGI) software.
UPDATED param_description with Association of proteins within efflux protein complexes or regulatory networks are encoded by the efflux pump components parameter: model_id,model_id,model_id, etc.
"
2680	UPDATE	MexAB-OprM with prematurely terminated MexR conferring resistance to meropenem and ciprofloxacin	 sulfonamide antibiotic;  penem;  panipenem;  tetracycline antibiotic;  clavulanic acid;  meropenem;  antibiotic efflux;  resistance-nodulation-cell division (RND) antibiotic efflux pump;  aztreonam;  trimethoprim;  aminocoumarin antibiotic;  cephalosporin;  macrolide antibiotic;  carbapenem;  ceftazidime;  ciprofloxacin;  cephamycin;  ceftriaxone;  amoxicillin-clavulanic acid;  colistin B;  colistin A;  peptide antibiotic;  diaminopyrimidine antibiotic;  ampicillin;  amoxicillin;  penam;  sulfamethoxazole;  novobiocin;  efflux pump complex or subunit conferring antibiotic resistance;  trimethoprim-sulfamethoxazole;  tetracycline;  monobactam;  fluoroquinolone antibiotic;  erythromycin;  phenicol antibiotic;  azithromycin;  chloramphenicol; 	model_description; model_param	"UPDATED model_description with Efflux Pump System Meta-Models (EPS) are dedicated to efflux complexes and their regulators, such as AcrAB-TolC. Using the efflux pump components parameter, this model type simply includes a list of detection models for each component of the complex. This model type is still under development and not currently supported by the Resistance Gene Identifier (RGI) software.
UPDATED param_description with Association of proteins within efflux protein complexes or regulatory networks are encoded by the efflux pump components parameter: model_id,model_id,model_id, etc.
"
2681	UPDATE	Escherichia coli fabG mutations conferring resistance to triclosan	 antibiotic target alteration;  antibiotic resistant fabG;  triclosan;  disinfecting agents and antiseptics; 	model_description; model_param	"UPDATED model_description with Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
"
2682	UPDATE	MexAB-OprM with NalC mutations conferring resistance to aztreonam	 sulfonamide antibiotic;  penem;  panipenem;  tetracycline antibiotic;  clavulanic acid;  meropenem;  antibiotic efflux;  resistance-nodulation-cell division (RND) antibiotic efflux pump;  aztreonam;  trimethoprim;  aminocoumarin antibiotic;  cephalosporin;  macrolide antibiotic;  carbapenem;  ceftazidime;  ciprofloxacin;  cephamycin;  ceftriaxone;  amoxicillin-clavulanic acid;  colistin B;  colistin A;  peptide antibiotic;  diaminopyrimidine antibiotic;  ampicillin;  amoxicillin;  penam;  sulfamethoxazole;  novobiocin;  efflux pump complex or subunit conferring antibiotic resistance;  trimethoprim-sulfamethoxazole;  tetracycline;  monobactam;  fluoroquinolone antibiotic;  erythromycin;  phenicol antibiotic;  azithromycin;  chloramphenicol; 	model_description; model_param	"UPDATED model_description with Efflux Pump System Meta-Models (EPS) are dedicated to efflux complexes and their regulators, such as AcrAB-TolC. Using the efflux pump components parameter, this model type simply includes a list of detection models for each component of the complex. This model type is still under development and not currently supported by the Resistance Gene Identifier (RGI) software.
UPDATED param_description with Association of proteins within efflux protein complexes or regulatory networks are encoded by the efflux pump components parameter: model_id,model_id,model_id, etc.
"
2683	UPDATE	MexAB-OprM with NalD mutations conferring resistance to multiple antibiotics	 sulfonamide antibiotic;  penem;  panipenem;  tetracycline antibiotic;  clavulanic acid;  meropenem;  antibiotic efflux;  resistance-nodulation-cell division (RND) antibiotic efflux pump;  aztreonam;  nalidixic acid;  aminocoumarin antibiotic;  cephalosporin;  macrolide antibiotic;  carbapenem;  ceftazidime;  ciprofloxacin;  cephamycin;  ceftriaxone;  amoxicillin-clavulanic acid;  colistin B;  colistin A;  peptide antibiotic;  diaminopyrimidine antibiotic;  ticarcillin;  ampicillin;  amoxicillin;  penam;  sulfamethoxazole;  novobiocin;  phenicol antibiotic;  efflux pump complex or subunit conferring antibiotic resistance;  trimethoprim-sulfamethoxazole;  tetracycline;  monobactam;  fluoroquinolone antibiotic;  erythromycin;  trimethoprim;  azithromycin;  chloramphenicol; 	model_description; model_param	"UPDATED model_description with Efflux Pump System Meta-Models (EPS) are dedicated to efflux complexes and their regulators, such as AcrAB-TolC. Using the efflux pump components parameter, this model type simply includes a list of detection models for each component of the complex. This model type is still under development and not currently supported by the Resistance Gene Identifier (RGI) software.
UPDATED param_description with Association of proteins within efflux protein complexes or regulatory networks are encoded by the efflux pump components parameter: model_id,model_id,model_id, etc.
"
1436	UPDATE	TEM-40	 penam;  antibiotic inactivation;  penem;  cephalosporin;  monobactam;  ampicillin;  TEM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
122	UPDATE	VIM-34	 penam;  antibiotic inactivation;  penem;  carbapenem;  cephalosporin;  cephamycin;  VIM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3999	UPDATE	TEM-236	 penam;  antibiotic inactivation;  penem;  cephalosporin;  monobactam;  ampicillin;  TEM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1437	UPDATE	AcrF	 penam;  antibiotic efflux;  resistance-nodulation-cell division (RND) antibiotic efflux pump;  efflux pump complex or subunit conferring antibiotic resistance;  cephalosporin;  cephamycin;  ciprofloxacin;  fluoroquinolone antibiotic; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
645	UPDATE	mecR1	 penam;  methicillin resistant PBP2;  methicillin;  antibiotic target replacement; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
43	UPDATE	tet(42)	 tetracycline antibiotic;  efflux pump complex or subunit conferring antibiotic resistance;  major facilitator superfamily (MFS) antibiotic efflux pump;  tetracycline;  antibiotic efflux; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3998	UPDATE	TEM-235	 penam;  antibiotic inactivation;  penem;  cephalosporin;  monobactam;  ampicillin;  TEM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5405	UPDATE	PDC-270	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
99	UPDATE	QnrB38	 sparfloxacin;  norfloxacin;  quinolone resistance protein (qnr);  gatifloxacin;  levofloxacin;  antibiotic target protection;  ciprofloxacin;  fluoroquinolone antibiotic;  nalidixic acid;  moxifloxacin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
98	UPDATE	CMY-48	 antibiotic inactivation;  CMY beta-lactamase;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2812	UPDATE	Mycobacteroides chelonae 23S rRNA with mutation conferring resistance to clarithromycin	 antibiotic target alteration;  23S rRNA with mutation conferring resistance to macrolide antibiotics;  clarithromycin;  macrolide antibiotic; 	model_description; model_param	"UPDATED model_description with Ribosomal RNA (rRNA) Gene Variant Models (RVM) are similar to Protein Variant Models (PVM), i.e. detect  sequences based on their similarity to a curated reference sequence and secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles, except RVMs are designed to detect AMR acquired via mutation of genes encoding ribosomal RNAs (rRNA). RVMs include a rRNA reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTN bit-score above the curated BLASTN cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTN bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
UPDATED param_description with The BLASTN bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
"
5404	UPDATE	PDC-268	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
91	UPDATE	gadX	 penam;  antibiotic efflux;  resistance-nodulation-cell division (RND) antibiotic efflux pump;  protein(s) and two-component regulatory system modulating antibiotic efflux;  norfloxacin;  macrolide antibiotic;  efflux pump complex or subunit conferring antibiotic resistance;  oxacillin;  cloxacillin;  fluoroquinolone antibiotic;  erythromycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
90	UPDATE	Staphylococcus aureus rpoB mutants conferring resistance to rifampicin	 rifampin;  rifapentine;  rifabutin;  rifamycin-resistant beta-subunit of RNA polymerase (rpoB);  antibiotic target replacement;  antibiotic target alteration;  rifaximin;  rifamycin antibiotic; 	model_description; model_param	"UPDATED model_description with Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
"
93	UPDATE	SHV-105	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  SHV beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
92	UPDATE	CTX-M-42	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
95	UPDATE	CMY-56	 antibiotic inactivation;  CMY beta-lactamase;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
94	UPDATE	CMY-79	 antibiotic inactivation;  CMY beta-lactamase;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
97	UPDATE	vanXY gene in vanC cluster	 glycopeptide antibiotic;  glycopeptide resistance gene cluster;  antibiotic target alteration;  vancomycin;  vanXY; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with vancomycin
UPDATED category_aro_cvterm_id with 35947
UPDATED category_aro_accession with 0000028
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.
UPDATED param_value with 125
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
96	UPDATE	OXA-426	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1623	UPDATE	GIM-2	 penam;  GIM beta-lactamase;  penem;  carbapenem;  cephalosporin;  antibiotic inactivation;  cephamycin;  monobactam; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1990	UPDATE	CMY-82	 antibiotic inactivation;  CMY beta-lactamase;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1993	UPDATE	QnrB74	 sparfloxacin;  norfloxacin;  quinolone resistance protein (qnr);  gatifloxacin;  levofloxacin;  antibiotic target protection;  ciprofloxacin;  fluoroquinolone antibiotic;  nalidixic acid;  moxifloxacin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1620	UPDATE	CTX-M-156	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1627	UPDATE	CTX-M-95	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1994	UPDATE	gimA	 antibiotic inactivation;  methymycin;  oleandomycin;  chalcomycin;  gimA family macrolide glycosyltransferase;  macrolide antibiotic;  tylosin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1625	UPDATE	OXA-179	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1624	UPDATE	lmrD	 efflux pump complex or subunit conferring antibiotic resistance;  ATP-binding cassette (ABC) antibiotic efflux pump;  antibiotic efflux;  lincosamide antibiotic; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1999	UPDATE	TEM-215	 penam;  antibiotic inactivation;  penem;  cephalosporin;  monobactam;  ampicillin;  TEM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1998	UPDATE	CTX-M-83	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1629	UPDATE	TEM-197	 penam;  antibiotic inactivation;  penem;  cephalosporin;  monobactam;  ampicillin;  TEM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1628	UPDATE	SHV-154	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  SHV beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
349	UPDATE	vanL	 glycopeptide antibiotic;  glycopeptide resistance gene cluster;  Van ligase;  vancomycin;  antibiotic target alteration; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with vancomycin
UPDATED category_aro_cvterm_id with 35947
UPDATED category_aro_accession with 0000028
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.
UPDATED param_value with 275
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3535	UPDATE	OXA-473	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3534	UPDATE	OXA-472	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2860	UPDATE	PDC-81	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2861	UPDATE	PDC-82	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2862	UPDATE	PDC-83	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2863	UPDATE	PDC-84	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
559	UPDATE	vanXY gene in vanE cluster	 glycopeptide antibiotic;  glycopeptide resistance gene cluster;  antibiotic target alteration;  vancomycin;  vanXY; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with vancomycin
UPDATED category_aro_cvterm_id with 35947
UPDATED category_aro_accession with 0000028
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.
UPDATED param_value with 125
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
558	UPDATE	qacB	 efflux pump complex or subunit conferring antibiotic resistance;  fluoroquinolone antibiotic;  major facilitator superfamily (MFS) antibiotic efflux pump;  antibiotic efflux; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2866	UPDATE	PDC-87	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2867	UPDATE	PDC-88	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
555	UPDATE	OXA-133	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
554	UPDATE	OXA-163	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
557	UPDATE	SHV-9	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  SHV beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
556	UPDATE	vanY gene in vanB cluster	 glycopeptide antibiotic;  glycopeptide resistance gene cluster;  antibiotic target alteration;  vancomycin;  vanY; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with vancomycin
UPDATED category_aro_cvterm_id with 35947
UPDATED category_aro_accession with 0000028
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.
UPDATED param_value with 50
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
551	UPDATE	CTX-M-117	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
550	UPDATE	CMY-71	 antibiotic inactivation;  CMY beta-lactamase;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
553	UPDATE	VIM-35	 penam;  antibiotic inactivation;  penem;  carbapenem;  cephalosporin;  cephamycin;  VIM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
552	UPDATE	QnrB28	 sparfloxacin;  norfloxacin;  quinolone resistance protein (qnr);  gatifloxacin;  levofloxacin;  antibiotic target protection;  ciprofloxacin;  fluoroquinolone antibiotic;  nalidixic acid;  moxifloxacin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5054	UPDATE	OXA-745	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1438	UPDATE	SHV-19	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  SHV beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5055	UPDATE	OXA-746	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1439	UPDATE	SHV-80	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  SHV beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1199	UPDATE	SHV-168	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  SHV beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1198	UPDATE	mef(B)	 efflux pump complex or subunit conferring antibiotic resistance;  major facilitator superfamily (MFS) antibiotic efflux pump;  macrolide antibiotic;  antibiotic efflux; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3348	UPDATE	cfr(B)	 chloramphenicol;  linezolid;  oxazolidinone antibiotic;  antibiotic target alteration;  streptogramin antibiotic;  clindamycin;  phenicol antibiotic;  Cfr 23S ribosomal RNA methyltransferase;  lincosamide antibiotic; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3349	UPDATE	tet(U)	 tetracycline antibiotic;  efflux pump complex or subunit conferring antibiotic resistance;  major facilitator superfamily (MFS) antibiotic efflux pump;  tetracycline;  antibiotic efflux; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2643	UPDATE	tetA(46)	 tetracycline antibiotic;  efflux pump complex or subunit conferring antibiotic resistance;  ATP-binding cassette (ABC) antibiotic efflux pump;  tetracycline;  antibiotic efflux; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1191	UPDATE	mdtM	 antibiotic efflux;  major facilitator superfamily (MFS) antibiotic efflux pump;  norfloxacin;  disinfecting agents and antiseptics;  efflux pump complex or subunit conferring antibiotic resistance;  lincomycin;  puromycin;  acriflavine;  nucleoside antibiotic;  fluoroquinolone antibiotic;  lincosamide antibiotic;  phenicol antibiotic;  chloramphenicol; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1190	UPDATE	OXA-354	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1193	UPDATE	ErmH	 carbomycin;  pristinamycin IC;  Erm 23S ribosomal RNA methyltransferase;  oleandomycin;  macrolide antibiotic;  streptogramin B antibiotic;  lincomycin;  antibiotic target alteration;  streptogramin antibiotic;  lincosamide antibiotic;  erythromycin; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with carbomycin
UPDATED category_aro_cvterm_id with 37627
UPDATED category_aro_accession with 3001228
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Produced by Streptomyces halstedii and Streptomyces thermotolerans.
UPDATED category_aro_name with pristinamycin IC
UPDATED category_aro_cvterm_id with 37022
UPDATED category_aro_accession with 3000678
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Pristinamycin IC is a class B streptogramin derived from virginiamycin S1.
UPDATED category_aro_name with oleandomycin
UPDATED category_aro_cvterm_id with 37247
UPDATED category_aro_accession with 3000867
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Oleandomycin is a 14-membered macrolide produced by Streptomyces antibioticus. It is ssimilar to erythromycin, and contains a desosamine amino sugar and an oleandrose sugar. It targets the 50S ribosomal subunit to prevent protein synthesis.
UPDATED category_aro_name with streptogramin B antibiotic
UPDATED category_aro_cvterm_id with 35967
UPDATED category_aro_accession with 0000050
UPDATED category_aro_class_name with Drug Class
UPDATED category_aro_description with Streptogramin B antibiotics are are cyclic hepta- or hexa-depsipeptides.  Type B streptogramins block the peptide exit tunnel of the 50S bacterial ribosome. The general composition of group B streptogramins is 3-hydroxypicolinic acid-L-Thr-D-aminobutyric acid (or D-Ala)-L-Pro-L-Phe (or 4-N-,N-(dimethylamino)-L-Phe)-X-L-phenylglycine. Used alone, streptogramin B antibiotics are bacteriostatic, but is bactericidal when used with streptogramin A antibiotics.
UPDATED category_aro_name with lincomycin
UPDATED category_aro_cvterm_id with 35964
UPDATED category_aro_accession with 0000046
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Lincomycin is a lincosamide antibiotic that comes from the actinomyces Streptomyces lincolnensis. It binds to the 23s portion of the 50S subunit of bacterial ribosomes and inhibit early elongation of peptide chain by inhibiting transpeptidase reaction.
UPDATED category_aro_name with erythromycin
UPDATED category_aro_cvterm_id with 35925
UPDATED category_aro_accession with 0000006
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure/function processes critical for life or replication are inhibited.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1192	UPDATE	VEB-1	 antibiotic inactivation;  monobactam;  cephalosporin;  VEB beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1195	UPDATE	SHV-55	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  SHV beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1194	UPDATE	OXA-16	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1197	UPDATE	Mycobacterium tuberculosis rpsL mutations conferring resistance to Streptomycin	 antibiotic target alteration;  antibiotic-resistant rpsL;  streptomycin;  aminoglycoside antibiotic; 	model_description; model_param	"UPDATED model_description with Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
"
1196	UPDATE	OXA-71	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1759	UPDATE	vanF	 glycopeptide antibiotic;  glycopeptide resistance gene cluster;  Van ligase;  vancomycin;  antibiotic target alteration; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with vancomycin
UPDATED category_aro_cvterm_id with 35947
UPDATED category_aro_accession with 0000028
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.
UPDATED param_value with 350
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1758	UPDATE	OXA-326	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1757	UPDATE	emrA	 efflux pump complex or subunit conferring antibiotic resistance;  nalidixic acid;  major facilitator superfamily (MFS) antibiotic efflux pump;  fluoroquinolone antibiotic;  antibiotic efflux; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1756	UPDATE	CMY-93	 antibiotic inactivation;  CMY beta-lactamase;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1755	UPDATE	CTX-M-23	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1754	UPDATE	vanO	 glycopeptide antibiotic;  glycopeptide resistance gene cluster;  Van ligase;  vancomycin;  antibiotic target alteration; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with vancomycin
UPDATED category_aro_cvterm_id with 35947
UPDATED category_aro_accession with 0000028
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.
UPDATED param_value with 350
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1753	UPDATE	SHV-148	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  SHV beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1752	UPDATE	MdtK	 efflux pump complex or subunit conferring antibiotic resistance;  fluoroquinolone antibiotic;  antibiotic efflux;  multidrug and toxic compound extrusion (MATE) transporter;  ciprofloxacin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1751	UPDATE	Erm(33)	 streptogramin A antibiotic;  antibiotic target alteration;  virginiamycin S2;  vernamycin C;  pristinamycin IC;  patricin B;  patricin A;  oleandomycin;  ostreogrycin B3;  macrolide antibiotic;  telithromycin;  tylosin;  lincosamide antibiotic;  dirithromycin;  clarithromycin;  clindamycin;  dalfopristin;  pristinamycin IB;  quinupristin;  pristinamycin IA;  Erm 23S ribosomal RNA methyltransferase;  virginiamycin M1;  madumycin II;  griseoviridin;  streptogramin B antibiotic;  lincomycin;  streptogramin antibiotic;  roxithromycin;  spiramycin;  azithromycin;  erythromycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1750	UPDATE	OXA-254	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1177	UPDATE	KPC-12	 antibiotic inactivation;  penam;  carbapenem;  cephalosporin;  monobactam;  KPC beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1176	UPDATE	Mycobacterium tuberculosis katG mutations conferring resistance to isoniazid	 antibiotic target alteration;  isoniazid resistant katG;  isoniazid-like antibiotic; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
DELETED 36659
UPDATED category_aro_name with isoniazid-like antibiotic
UPDATED category_aro_cvterm_id with 45734
UPDATED category_aro_accession with 3007152
UPDATED category_aro_class_name with Drug Class
UPDATED category_aro_description with A group of antibiotics containing isoniazid and its derivatives.
UPDATED param_description with A nucleotide substitution resulting in a change from an amino acid codon to a STOP codon, encoded as [wild type amino acid][position][STOP], for example Q42STOP.
UPDATED param_description with A subtype of the insertion mutation detection model parameter used when a set of insertion mutations are reported in a nucleotide sequence format, encoded as [+]nt[position]:[nucleotides], for example +nt391:GG. Such mutations may be of variable length, possibly causing a frameshift but not causing premature termination or a functional knockout.
UPDATED param_description with A subtype of the deletion mutation detection model parameter used when a set of deletion mutations are reported in a nucleotide sequence format, encoded as [-]nt[position]:[nucleotides], for example -nt25:T.
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
UPDATED param_description with A set of nucleotide or amino acid substitutions that are all required to confer resistance to an antibiotic drug or drug class, encoded as: [wild-type 1][position 1][mutation 1],[wild-type 2][position 2][mutation 2], etc. For example, D63Y,T142K.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1175	UPDATE	Enterococcus faecium cls conferring resistance to daptomycin	 peptide antibiotic;  antibiotic target alteration;  daptomycin resistant cls;  daptomycin; 	model_description; model_param	"UPDATED model_description with Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
UPDATED param_description with A subtype of the insertion mutation detection model parameter is used when a set of insertion mutations are reported in a peptide sequence format, encoded as [+][AAs][position range], for example +D345 or +MPL110-112.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
"
1174	UPDATE	QnrB22	 sparfloxacin;  norfloxacin;  quinolone resistance protein (qnr);  gatifloxacin;  levofloxacin;  antibiotic target protection;  ciprofloxacin;  fluoroquinolone antibiotic;  nalidixic acid;  moxifloxacin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1173	UPDATE	TEM-54	 penam;  antibiotic inactivation;  penem;  cephalosporin;  monobactam;  ampicillin;  TEM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1172	UPDATE	OXA-194	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1171	UPDATE	tet(44)	 chlortetracycline;  demeclocycline;  oxytetracycline;  tetracycline antibiotic;  tetracycline;  antibiotic target protection;  minocycline;  tetracycline-resistant ribosomal protection protein;  doxycycline; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1170	UPDATE	CMY-46	 antibiotic inactivation;  CMY beta-lactamase;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4251	UPDATE	ADC-186	 antibiotic inactivation;  cephalosporin;  ADC beta-lactamases pending classification for carbapenemase activity; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4250	UPDATE	ADC-185	 antibiotic inactivation;  cephalosporin;  ADC beta-lactamases pending classification for carbapenemase activity; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4253	UPDATE	ADC-188	 antibiotic inactivation;  cephalosporin;  ADC beta-lactamases pending classification for carbapenemase activity; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4252	UPDATE	ADC-187	 antibiotic inactivation;  cephalosporin;  ADC beta-lactamases pending classification for carbapenemase activity; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4255	UPDATE	ADC-190	 antibiotic inactivation;  cephalosporin;  ADC beta-lactamases pending classification for carbapenemase activity; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4254	UPDATE	ADC-189	 antibiotic inactivation;  cephalosporin;  ADC beta-lactamases pending classification for carbapenemase activity; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1179	UPDATE	IMP-4	 penam;  antibiotic inactivation;  penem;  carbapenem;  cephalosporin;  IMP beta-lactamase;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1178	UPDATE	CMY-81	 antibiotic inactivation;  CMY beta-lactamase;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5533	UPDATE	PDC-403	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5532	UPDATE	PDC-402	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5531	UPDATE	PDC-401	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5530	UPDATE	PDC-400	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5537	UPDATE	PDC-407	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5536	UPDATE	PDC-406	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5535	UPDATE	PDC-405	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5534	UPDATE	PDC-404	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5539	UPDATE	PDC-409	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5538	UPDATE	PDC-408	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
513	UPDATE	CARB-19	 penam;  antibiotic inactivation;  CARB beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
644	UPDATE	OXY-2-1	 penam;  OXY beta-lactamase;  cephalosporin;  antibiotic inactivation;  monobactam; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1285	UPDATE	SAT-2	 streptothricin acetyltransferase (SAT);  streptothricin;  antibiotic inactivation;  nucleoside antibiotic; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1284	UPDATE	IND-15	 carbapenem;  antibiotic inactivation;  IND beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1287	UPDATE	CTX-M-110	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1004	UPDATE	vanR gene in vanD cluster	 vanR;  glycopeptide resistance gene cluster;  teicoplanin;  glycopeptide antibiotic;  antibiotic target alteration;  vancomycin; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with vancomycin
UPDATED category_aro_cvterm_id with 35947
UPDATED category_aro_accession with 0000028
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.
UPDATED category_aro_name with teicoplanin
UPDATED category_aro_cvterm_id with 35948
UPDATED category_aro_accession with 0000029
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Teicoplanin is a glycopeptide antibiotic used in the prophylaxis and treatment of serious infections caused by Gram-positive bacteria. Teicoplanin has a unique acyl-aliphatic chain, and binds to cell wall precursors to inhibit transglycosylation  and transpeptidation.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1281	UPDATE	OXA-110	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1280	UPDATE	QnrB12	 sparfloxacin;  norfloxacin;  quinolone resistance protein (qnr);  gatifloxacin;  levofloxacin;  antibiotic target protection;  ciprofloxacin;  fluoroquinolone antibiotic;  nalidixic acid;  moxifloxacin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1283	UPDATE	KPC-6	 antibiotic inactivation;  penam;  carbapenem;  cephalosporin;  monobactam;  KPC beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1282	UPDATE	SIM-1	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  SIM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1003	UPDATE	OXA-18	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1289	UPDATE	OKP-B-7	 penam;  antibiotic inactivation;  OKP beta-lactamase;  cephalosporin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1288	UPDATE	OXA-82	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1002	UPDATE	AAC(6')-Ib4	 AAC(6');  antibiotic inactivation;  aminoglycoside antibiotic;  gentamicin A; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with gentamicin A
UPDATED category_aro_cvterm_id with 40942
UPDATED category_aro_accession with 3004015
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Gentamicin A is part of a complex of broad spectrum aminoglycoside antibiotics. Gentamicin inhibits protein synthesis, resulting in bacterial cell death.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
876	UPDATE	smeE	 antibiotic efflux;  resistance-nodulation-cell division (RND) antibiotic efflux pump;  macrolide antibiotic;  efflux pump complex or subunit conferring antibiotic resistance;  tetracycline antibiotic;  fluoroquinolone antibiotic;  phenicol antibiotic;  tetracycline;  chloramphenicol; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1579	UPDATE	QnrB9	 sparfloxacin;  norfloxacin;  quinolone resistance protein (qnr);  gatifloxacin;  levofloxacin;  antibiotic target protection;  ciprofloxacin;  fluoroquinolone antibiotic;  nalidixic acid;  moxifloxacin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1578	UPDATE	SHV-123	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  SHV beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
689	UPDATE	CTX-M-123	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
688	UPDATE	MOX-2	 penam;  antibiotic inactivation;  MOX beta-lactamase;  cephamycin;  cephalosporin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1872	UPDATE	vanXY gene in vanL cluster	 glycopeptide antibiotic;  glycopeptide resistance gene cluster;  antibiotic target alteration;  vancomycin;  vanXY; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with vancomycin
UPDATED category_aro_cvterm_id with 35947
UPDATED category_aro_accession with 0000028
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.
UPDATED param_value with 125
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
877	UPDATE	SHV-124	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  SHV beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
685	UPDATE	OXA-239	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
684	UPDATE	SHV-37	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  SHV beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
687	UPDATE	APH(3')-Vc	 antibiotic inactivation;  aminoglycoside antibiotic;  paromomycin;  APH(3');  ribostamycin;  G418;  neomycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
686	UPDATE	OXA-162	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
681	UPDATE	TEM-120	 penam;  antibiotic inactivation;  penem;  cephalosporin;  monobactam;  ampicillin;  TEM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
680	UPDATE	CMY-54	 antibiotic inactivation;  CMY beta-lactamase;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
683	UPDATE	CMY-75	 antibiotic inactivation;  CMY beta-lactamase;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
682	UPDATE	QnrS4	 sparfloxacin;  norfloxacin;  quinolone resistance protein (qnr);  gatifloxacin;  levofloxacin;  antibiotic target protection;  ciprofloxacin;  fluoroquinolone antibiotic;  nalidixic acid;  moxifloxacin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1227	UPDATE	aadA2	 antibiotic inactivation;  aminoglycoside antibiotic;  ANT(3'');  streptomycin;  spectinomycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
875	UPDATE	dfrA19	 trimethoprim;  diaminopyrimidine antibiotic;  trimethoprim resistant dihydrofolate reductase dfr;  antibiotic target replacement; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4188	UPDATE	ADC-114	 antibiotic inactivation;  cephalosporin;  ADC beta-lactamases pending classification for carbapenemase activity; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
469	UPDATE	SHV-49	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  SHV beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
872	UPDATE	vatC	 dalfopristin;  antibiotic inactivation;  streptogramin vat acetyltransferase;  virginiamycin M1;  madumycin II;  griseoviridin;  streptogramin A antibiotic;  streptogramin antibiotic; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1225	UPDATE	TEM-178	 penam;  antibiotic inactivation;  penem;  cephalosporin;  monobactam;  ampicillin;  TEM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3435	UPDATE	OXA-268	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
620	UPDATE	OXA-320	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
870	UPDATE	otr(B)	 tetracycline antibiotic;  efflux pump complex or subunit conferring antibiotic resistance;  major facilitator superfamily (MFS) antibiotic efflux pump;  tetracycline;  antibiotic efflux; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2131	UPDATE	Mycobacterium tuberculosis 16S rRNA mutation conferring resistance to streptomycin	 antibiotic target alteration;  streptomycin;  aminoglycoside antibiotic;  16s rRNA with mutation conferring resistance to aminoglycoside antibiotics; 	model_description; model_param	"UPDATED model_description with Ribosomal RNA (rRNA) Gene Variant Models (RVM) are similar to Protein Variant Models (PVM), i.e. detect  sequences based on their similarity to a curated reference sequence and secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles, except RVMs are designed to detect AMR acquired via mutation of genes encoding ribosomal RNAs (rRNA). RVMs include a rRNA reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTN bit-score above the curated BLASTN cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTN bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
UPDATED param_description with The BLASTN bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
"
1223	UPDATE	vph	 peptide antibiotic;  viomycin phosphotransferase;  antibiotic inactivation;  viomycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
871	UPDATE	CGB-1	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  CGB beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1222	UPDATE	FosA	 fosfomycin;  fosfomycin thiol transferase;  antibiotic inactivation;  phosphonic acid antibiotic; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_name with phosphonic acid antibiotic
UPDATED category_aro_cvterm_id with 45731
UPDATED category_aro_accession with 3007149
UPDATED category_aro_class_name with Drug Class
UPDATED category_aro_description with A group of antibiotics derived from phosphonic acids.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2037	UPDATE	tet(T)	 chlortetracycline;  demeclocycline;  oxytetracycline;  tetracycline antibiotic;  tetracycline;  antibiotic target protection;  minocycline;  tetracycline-resistant ribosomal protection protein;  doxycycline; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4389	UPDATE	BlaB-28	 carbapenem;  penam;  antibiotic inactivation;  BlaB beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4388	UPDATE	BlaB-27	 carbapenem;  penam;  antibiotic inactivation;  BlaB beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
625	UPDATE	QnrB46	 sparfloxacin;  norfloxacin;  quinolone resistance protein (qnr);  gatifloxacin;  levofloxacin;  antibiotic target protection;  ciprofloxacin;  fluoroquinolone antibiotic;  nalidixic acid;  moxifloxacin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5629	UPDATE	PLN-1	 carbapenem;  antibiotic inactivation;  PLN beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5628	UPDATE	PLA-6	 carbapenem;  antibiotic inactivation;  cephalosporin;  PLA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4383	UPDATE	BlaB-22	 carbapenem;  penam;  antibiotic inactivation;  BlaB beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4382	UPDATE	BlaB-20	 carbapenem;  penam;  antibiotic inactivation;  BlaB beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4381	UPDATE	BlaB-2	 carbapenem;  penam;  antibiotic inactivation;  BlaB beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1220	UPDATE	OCH-5	 penam;  antibiotic inactivation;  penem;  cephalosporin;  cephamycin;  monobactam;  OCH beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4387	UPDATE	BlaB-26	 carbapenem;  penam;  antibiotic inactivation;  BlaB beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5622	UPDATE	PFM-1	 carbapenem;  antibiotic inactivation;  PFM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4385	UPDATE	BlaB-24	 carbapenem;  penam;  antibiotic inactivation;  BlaB beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4384	UPDATE	BlaB-23	 carbapenem;  penam;  antibiotic inactivation;  BlaB beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
407	UPDATE	OXA-352	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
406	UPDATE	ACC-4	 penam;  monobactam;  cephalosporin;  ACC beta-lactamase;  antibiotic inactivation; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1373	UPDATE	CMY-26	 antibiotic inactivation;  CMY beta-lactamase;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1372	UPDATE	ANT(2'')-Ia	 antibiotic inactivation;  plazomicin;  kanamycin A;  ANT(2'');  gentamicin B;  gentamicin C;  aminoglycoside antibiotic;  tobramycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1375	UPDATE	CMY-11	 antibiotic inactivation;  CMY beta-lactamase;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
402	UPDATE	tet(Y)	 tetracycline antibiotic;  efflux pump complex or subunit conferring antibiotic resistance;  major facilitator superfamily (MFS) antibiotic efflux pump;  tetracycline;  antibiotic efflux; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1377	UPDATE	CTX-M-60	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
400	UPDATE	PDC-1	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1379	UPDATE	OXA-313	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1378	UPDATE	AAC(3)-IIc	 antibiotic inactivation;  AAC(3);  paromomycin;  kanamycin A;  aminoglycoside antibiotic;  neomycin;  butirosin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
629	UPDATE	VIM-28	 penam;  antibiotic inactivation;  penem;  carbapenem;  cephalosporin;  cephamycin;  VIM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
409	UPDATE	vanR gene in vanL cluster	 glycopeptide antibiotic;  glycopeptide resistance gene cluster;  antibiotic target alteration;  vanR;  vancomycin; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with vancomycin
UPDATED category_aro_cvterm_id with 35947
UPDATED category_aro_accession with 0000028
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
408	UPDATE	OXA-380	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3834	UPDATE	Mycobacterium tuberculosis katG mutations conferring resistance to prothionamide	 thioamide antibiotic;  antibiotic target alteration;  prothionamide resistant katG; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
DELETED 40958
UPDATED category_aro_name with thioamide antibiotic
UPDATED category_aro_cvterm_id with 45738
UPDATED category_aro_accession with 3007156
UPDATED category_aro_class_name with Drug Class
UPDATED category_aro_description with A group of antibiotics possessing the thioamide functional group.
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A subtype of the deletion mutation detection model parameter used when a set of deletion mutations are reported in a nucleotide sequence format, encoded as [-]nt[position]:[nucleotides], for example -nt25:T.
UPDATED param_description with A set of nucleotide or amino acid substitutions that are all required to confer resistance to an antibiotic drug or drug class, encoded as: [wild-type 1][position 1][mutation 1],[wild-type 2][position 2][mutation 2], etc. For example, D63Y,T142K.
"
3836	UPDATE	Mycobacterium tuberculosis ethA mutations conferring resistance to isoniazid	 antibiotic target alteration;  isoniazid-like antibiotic;  isoniazid resistant ethA; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
DELETED 36659
UPDATED category_aro_name with isoniazid-like antibiotic
UPDATED category_aro_cvterm_id with 45734
UPDATED category_aro_accession with 3007152
UPDATED category_aro_class_name with Drug Class
UPDATED category_aro_description with A group of antibiotics containing isoniazid and its derivatives.
UPDATED param_description with A nucleotide substitution resulting in a change from an amino acid codon to a STOP codon, encoded as [wild type amino acid][position][STOP], for example Q42STOP.
UPDATED param_description with A subtype of the insertion mutation detection model parameter used when a set of insertion mutations are reported in a nucleotide sequence format, encoded as [+]nt[position]:[nucleotides], for example +nt391:GG. Such mutations may be of variable length, possibly causing a frameshift but not causing premature termination or a functional knockout.
UPDATED param_description with A subtype of the deletion mutation detection model parameter used when a set of deletion mutations are reported in a nucleotide sequence format, encoded as [-]nt[position]:[nucleotides], for example -nt25:T.
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
UPDATED param_description with A set of nucleotide or amino acid substitutions that are all required to confer resistance to an antibiotic drug or drug class, encoded as: [wild-type 1][position 1][mutation 1],[wild-type 2][position 2][mutation 2], etc. For example, D63Y,T142K.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
628	UPDATE	catB10	 antibiotic inactivation;  thiamphenicol;  chloramphenicol acetyltransferase (CAT);  azidamfenicol;  phenicol antibiotic;  chloramphenicol; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3830	UPDATE	qacL	 efflux pump complex or subunit conferring antibiotic resistance;  small multidrug resistance (SMR) antibiotic efflux pump;  disinfecting agents and antiseptics;  antibiotic efflux; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3831	UPDATE	23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(A)	 Erm 23S ribosomal RNA methyltransferase;  macrolide antibiotic;  antibiotic target alteration;  streptogramin antibiotic;  erythromycin;  lincosamide antibiotic; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with erythromycin
UPDATED category_aro_cvterm_id with 35925
UPDATED category_aro_accession with 0000006
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure/function processes critical for life or replication are inhibited.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3832	UPDATE	FosB2	 antibiotic inactivation;  fosfomycin thiol transferase;  phosphonic acid antibiotic; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
DELETED 35944
UPDATED category_aro_name with phosphonic acid antibiotic
UPDATED category_aro_cvterm_id with 45731
UPDATED category_aro_accession with 3007149
UPDATED category_aro_class_name with Drug Class
UPDATED category_aro_description with A group of antibiotics derived from phosphonic acids.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1242	UPDATE	aadA6/aadA10	 antibiotic inactivation;  aminoglycoside antibiotic;  ANT(3'');  streptomycin;  spectinomycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1344	UPDATE	MexH	 antibiotic efflux;  resistance-nodulation-cell division (RND) antibiotic efflux pump;  norfloxacin;  efflux pump complex or subunit conferring antibiotic resistance;  acriflavine;  tetracycline antibiotic;  fluoroquinolone antibiotic;  disinfecting agents and antiseptics;  tetracycline; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2030	UPDATE	AAC(3)-IXa	 antibiotic inactivation;  AAC(3);  aminoglycoside antibiotic;  neomycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3838	UPDATE	Mycobacterium tuberculosis mshA mutations conferring resistance to prothionamide	 thioamide antibiotic;  antibiotic target alteration;  prothionamide resistant mshA; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
DELETED 40958
UPDATED category_aro_name with thioamide antibiotic
UPDATED category_aro_cvterm_id with 45738
UPDATED category_aro_accession with 3007156
UPDATED category_aro_class_name with Drug Class
UPDATED category_aro_description with A group of antibiotics possessing the thioamide functional group.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
"
3839	UPDATE	blaS1	 penam;  antibiotic inactivation;  mezlocillin;  cefixime;  blaS;  cephalosporin;  cephamycin;  oxacillin;  carbenicillin;  ampicillin;  piperacillin;  ceftriaxone;  cefoxitin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3452	UPDATE	OXA-288	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4031	UPDATE	PDC-183	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2749	UPDATE	lnuG	 antibiotic inactivation;  lincosamide nucleotidyltransferase (LNU);  lincomycin;  lincosamide antibiotic; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4033	UPDATE	PDC-306	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4032	UPDATE	PDC-207	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4035	UPDATE	PDC-117	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1229	UPDATE	CTX-M-6	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4037	UPDATE	PDC-104	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2748	UPDATE	oqxAB	 antibiotic efflux;  resistance-nodulation-cell division (RND) antibiotic efflux pump;  trimethoprim;  efflux pump complex or subunit conferring antibiotic resistance;  diaminopyrimidine antibiotic;  tigecycline;  glycylcycline;  ciprofloxacin;  tetracycline antibiotic;  nitrofuran antibiotic;  fluoroquinolone antibiotic;  nitrofurantoin; 	model_description; model_param	"UPDATED model_description with Efflux Pump System Meta-Models (EPS) are dedicated to efflux complexes and their regulators, such as AcrAB-TolC. Using the efflux pump components parameter, this model type simply includes a list of detection models for each component of the complex. This model type is still under development and not currently supported by the Resistance Gene Identifier (RGI) software.
UPDATED param_description with Association of proteins within efflux protein complexes or regulatory networks are encoded by the efflux pump components parameter: model_id,model_id,model_id, etc.
"
4039	UPDATE	PDC-292	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4038	UPDATE	PDC-173	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1228	UPDATE	CMY-30	 antibiotic inactivation;  CMY beta-lactamase;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4598	UPDATE	EFM-1	 carbapenem;  antibiotic inactivation;  EFM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4599	UPDATE	ELM-1	 carbapenem;  antibiotic inactivation;  ELM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
379	UPDATE	OXA-148	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
378	UPDATE	TEM-214	 penam;  antibiotic inactivation;  penem;  cephalosporin;  monobactam;  ampicillin;  TEM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2039	UPDATE	CARB-18	 penam;  antibiotic inactivation;  CARB beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
371	UPDATE	SHV-8	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  SHV beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
373	UPDATE	MIR-3	 antibiotic inactivation;  monobactam;  cephalosporin;  MIR beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
372	UPDATE	qacA	 efflux pump complex or subunit conferring antibiotic resistance;  fluoroquinolone antibiotic;  major facilitator superfamily (MFS) antibiotic efflux pump;  antibiotic efflux; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
375	UPDATE	mdtH	 antibiotic efflux;  major facilitator superfamily (MFS) antibiotic efflux pump;  norfloxacin;  efflux pump complex or subunit conferring antibiotic resistance;  fluoroquinolone antibiotic;  enoxacin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
374	UPDATE	SHV-21	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  SHV beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
377	UPDATE	mepA	 antibiotic efflux;  multidrug and toxic compound extrusion (MATE) transporter;  efflux pump complex or subunit conferring antibiotic resistance;  tigecycline;  glycylcycline;  tetracycline antibiotic; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
376	UPDATE	lnuC	 antibiotic inactivation;  lincosamide nucleotidyltransferase (LNU);  lincomycin;  lincosamide antibiotic; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with lincomycin
UPDATED category_aro_cvterm_id with 35964
UPDATED category_aro_accession with 0000046
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Lincomycin is a lincosamide antibiotic that comes from the actinomyces Streptomyces lincolnensis. It binds to the 23s portion of the 50S subunit of bacterial ribosomes and inhibit early elongation of peptide chain by inhibiting transpeptidase reaction.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4739	UPDATE	KPC-80	 antibiotic inactivation;  penam;  carbapenem;  cephalosporin;  monobactam;  KPC beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4349	UPDATE	ADC-93	 antibiotic inactivation;  cephalosporin;  ADC beta-lactamases pending classification for carbapenemase activity; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2194	UPDATE	TriC	 efflux pump complex or subunit conferring antibiotic resistance;  triclosan;  antibiotic efflux;  resistance-nodulation-cell division (RND) antibiotic efflux pump;  disinfecting agents and antiseptics; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4348	UPDATE	ADC-92	 antibiotic inactivation;  cephalosporin;  ADC beta-lactamases pending classification for carbapenemase activity; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
393	UPDATE	QnrS5	 sparfloxacin;  norfloxacin;  quinolone resistance protein (qnr);  gatifloxacin;  levofloxacin;  antibiotic target protection;  ciprofloxacin;  fluoroquinolone antibiotic;  nalidixic acid;  moxifloxacin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
392	UPDATE	TUS-1	 carbapenem;  antibiotic inactivation;  TUS beta-lactamase;  cephamycin;  cephalosporin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
391	UPDATE	VIM-2	 penam;  antibiotic inactivation;  avibactam;  ceftolozane-tazobactam;  penem;  ceftazidime-avibactam;  cephalosporin;  carbapenem;  ceftazidime;  cephamycin;  VIM beta-lactamase;  tazobactam;  ceftolozane; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_description with Serine beta-lactamase inhibitor targeting class A, class C, and some class D enzymes.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
390	UPDATE	vanS gene in vanG cluster	 glycopeptide antibiotic;  vanS;  antibiotic target alteration;  vancomycin;  glycopeptide resistance gene cluster; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with vancomycin
UPDATED category_aro_cvterm_id with 35947
UPDATED category_aro_accession with 0000028
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
397	UPDATE	OXA-357	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
396	UPDATE	sul3	 sulfadiazine;  sulfadoxine;  sulfacetamide;  sulfadimidine;  mafenide;  sulfamethoxazole;  sulfisoxazole;  sulfonamide resistant sul;  antibiotic target replacement;  sulfamethizole;  sulfasalazine;  sulfonamide antibiotic; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
395	UPDATE	blaF	 penam;  amoxicillin;  antibiotic inactivation;  blaF family beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
394	UPDATE	OXA-130	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
399	UPDATE	MIR-16	 antibiotic inactivation;  monobactam;  cephalosporin;  MIR beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
398	UPDATE	TEM-71	 penam;  antibiotic inactivation;  penem;  cephalosporin;  monobactam;  ampicillin;  TEM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4345	UPDATE	ADC-89	 antibiotic inactivation;  cephalosporin;  ADC beta-lactamases pending classification for carbapenemase activity; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2308	UPDATE	Acinetobacter baumannii OprD conferring resistance to imipenem	 penam;  carbapenem;  imipenem;  penem;  reduced permeability to antibiotic;  Outer Membrane Porin (Opr);  cephalosporin;  cephamycin;  monobactam;  resistance by absence; 	model_description; model_param	"UPDATED model_description with Protein Knockout Models (PKM) reflect resistance by the absence of a gene product, most often deletion of a gene involved in antibiotic import, such as Vibrio cholerae OmpT. Like Protein Homolog Models (PHMs), PKMs include a reference sequence and a bitscore cut-off for detection using BLASTP but instead are designed to only report lack of detection under Perfect or Strict criteria. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff. This model type is still under development and not currently supported by the Resistance Gene Identifier (RGI) software.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4344	UPDATE	ADC-88	 antibiotic inactivation;  cephalosporin;  ADC beta-lactamases pending classification for carbapenemase activity; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4729	UPDATE	KPC-66	 antibiotic inactivation;  penam;  carbapenem;  cephalosporin;  monobactam;  KPC beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4728	UPDATE	KPC-65	 antibiotic inactivation;  penam;  carbapenem;  cephalosporin;  monobactam;  KPC beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3960	UPDATE	SHV-218	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  SHV beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2301	UPDATE	Enterococcus faecalis YybT with mutation conferring daptomycin resistance	 peptide antibiotic;  antibiotic target alteration;  daptomycin;  daptomycin resistant YybT; 	model_description; model_param	"UPDATED model_description with Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
"
2300	UPDATE	Acinetobacter baumannii ampC beta-lactamase	 penam;  antibiotic inactivation;  cephalosporin;  cefepime;  piperacillin;  ampC-type beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2303	UPDATE	bcr-1	 antibiotic efflux;  efflux pump complex or subunit conferring antibiotic resistance;  bicyclomycin-like antibiotic;  major facilitator superfamily (MFS) antibiotic efflux pump;  bicyclomycin; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_name with bicyclomycin-like antibiotic
UPDATED category_aro_cvterm_id with 45732
UPDATED category_aro_accession with 3007150
UPDATED category_aro_class_name with Drug Class
UPDATED category_aro_description with A group of antibiotics including bicyclomycin and its analogues.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4726	UPDATE	KPC-63	 antibiotic inactivation;  penam;  carbapenem;  cephalosporin;  monobactam;  KPC beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2305	UPDATE	Enterococcus faecalis gshF with mutation conferring daptomycin resistance	 peptide antibiotic;  antibiotic target alteration;  daptomycin;  daptomycin resistant gshF; 	model_description; model_param	"UPDATED model_description with Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
"
4720	UPDATE	KPC-44	 antibiotic inactivation;  penam;  carbapenem;  cephalosporin;  monobactam;  KPC beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2307	UPDATE	carO	 reduced permeability to antibiotic;  imipenem;  carbapenem;  CarO porin;  resistance by absence;  meropenem; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Knockout Models (PKM) reflect resistance by the absence of a gene product, most often deletion of a gene involved in antibiotic import, such as Vibrio cholerae OmpT. Like Protein Homolog Models (PHMs), PKMs include a reference sequence and a bitscore cut-off for detection using BLASTP but instead are designed to only report lack of detection under Perfect or Strict criteria. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff. This model type is still under development and not currently supported by the Resistance Gene Identifier (RGI) software.
UPDATED category_aro_name with imipenem
UPDATED category_aro_cvterm_id with 36309
UPDATED category_aro_accession with 3000170
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Imipenem is a broad-spectrum antibiotic and is usually taken with cilastatin, which prevents hydrolysis of imipenem by renal dehydropeptidase-I. It is resistant to hydrolysis by most other beta-lactamases. Notable exceptions are the KPC beta-lactamases and Ambler Class B enzymes.
UPDATED category_aro_name with meropenem
UPDATED category_aro_cvterm_id with 35990
UPDATED category_aro_accession with 0000073
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Meropenem is an ultra-broad spectrum injectable antibiotic used to treat a wide variety of infections, including meningitis and pneumonia. It is a beta-lactam and belongs to the subgroup of carbapenem, similar to imipenem and ertapenem.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4722	UPDATE	KPC-59	 antibiotic inactivation;  penam;  carbapenem;  cephalosporin;  monobactam;  KPC beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1358	UPDATE	VIM-24	 penam;  antibiotic inactivation;  penem;  carbapenem;  cephalosporin;  cephamycin;  VIM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4676	UPDATE	IMI-5	 carbapenem;  antibiotic inactivation;  IMI beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2335	UPDATE	ADC-2	 antibiotic inactivation;  cephalosporin;  ADC beta-lactamase without carbapenemase activity; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1246	UPDATE	AAC(2')-Ic	 antibiotic inactivation;  AAC(2');  arbekacin;  gentamicin B;  gentamicin C;  amikacin;  aminoglycoside antibiotic;  tobramycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5105	UPDATE	OXA-800	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3745	UPDATE	Mycobacterium tuberculosis 23S rRNA mutation conferring resistance to capreomycin	 antibiotic target alteration;  capreomycin;  aminoglycoside antibiotic;  23s rRNA with mutation conferring resistance to aminoglycoside antibiotics; 	model_description; model_param	"UPDATED model_description with Ribosomal RNA (rRNA) Gene Variant Models (RVM) are similar to Protein Variant Models (PVM), i.e. detect  sequences based on their similarity to a curated reference sequence and secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles, except RVMs are designed to detect AMR acquired via mutation of genes encoding ribosomal RNAs (rRNA). RVMs include a rRNA reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTN bit-score above the curated BLASTN cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTN bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
UPDATED param_description with The BLASTN bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
245	UPDATE	cmlA5	 antibiotic efflux;  efflux pump complex or subunit conferring antibiotic resistance;  major facilitator superfamily (MFS) antibiotic efflux pump;  phenicol antibiotic;  chloramphenicol; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
244	UPDATE	SHV-164	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  SHV beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
247	UPDATE	TEM-158	 penam;  antibiotic inactivation;  penem;  cephalosporin;  monobactam;  ampicillin;  TEM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
246	UPDATE	CTX-M-126	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
241	UPDATE	ACT-30	 antibiotic inactivation;  carbapenem;  penam;  ACT beta-lactamase;  cephalosporin;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
240	UPDATE	vanR gene in vanF cluster	 glycopeptide antibiotic;  glycopeptide resistance gene cluster;  antibiotic target alteration;  vanR;  vancomycin; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with vancomycin
UPDATED category_aro_cvterm_id with 35947
UPDATED category_aro_accession with 0000028
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
243	UPDATE	OXA-9	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
242	UPDATE	SHV-152	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  SHV beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4628	UPDATE	GES-45	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  GES beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4629	UPDATE	GES-46	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  GES beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
249	UPDATE	basS	 antibiotic efflux;  polymyxin B;  protein(s) and two-component regulatory system modulating antibiotic efflux;  pmr phosphoethanolamine transferase;  peptide antibiotic;  antibiotic target alteration; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with polymyxin B
UPDATED category_aro_cvterm_id with 36593
UPDATED category_aro_accession with 3000454
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Polymyxin B is mixture of mostly polymyxins B1 and B2, mainly used for resistant gram-negative infections. They are polypeptides with cationic detergent action on cell membranes.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
248	UPDATE	OKP-B-9	 penam;  antibiotic inactivation;  OKP beta-lactamase;  cephalosporin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2274	UPDATE	RlmA(II)	 mycinamicin;  macrolide antibiotic;  non-erm 23S ribosomal RNA methyltransferase (G748);  antibiotic target alteration;  tylosin;  lincosamide antibiotic; 	ARO_description; model_description; ARO_category; model_param	"UPDATED ARO_description with RlmA(II) is a methyltransferase found in Streptococcus pneumoniae and confers resistance to tylosin and mycinamicin. Specifically, this enzyme adds a methyl group to guanosine 748 (E. coli numbering) of 23S ribosomal RNA.
UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with mycinamicin
UPDATED category_aro_cvterm_id with 37623
UPDATED category_aro_accession with 3001224
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Produced by Micromonospora griseorubida.
UPDATED category_aro_name with tylosin
UPDATED category_aro_cvterm_id with 36284
UPDATED category_aro_accession with 3000145
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Tylosin is a 16-membered macrolide, naturally produced by Streptomyces fradiae. It interacts with the bacterial ribosome 50S subunit to inhibit protein synthesis.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2277	UPDATE	mphM	 antibiotic inactivation;  macrolide phosphotransferase (MPH);  macrolide antibiotic;  erythromycin; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with erythromycin
UPDATED category_aro_cvterm_id with 35925
UPDATED category_aro_accession with 0000006
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure/function processes critical for life or replication are inhibited.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2276	UPDATE	Staphylococcus aureus ileS with mutation conferring resistance to mupirocin	 antibiotic-resistant isoleucyl-tRNA synthetase (ileS);  antibiotic target alteration;  mupirocin-like antibiotic; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
DELETED 36693
UPDATED category_aro_name with mupirocin-like antibiotic
UPDATED category_aro_cvterm_id with 45733
UPDATED category_aro_accession with 3007151
UPDATED category_aro_class_name with Drug Class
UPDATED category_aro_description with A group of antibiotics including mupirocin and similar mixtures (such as those including pseudomonic acid A).
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
"
2271	UPDATE	Staphylococcus aureus mupB conferring resistance to mupirocin	 antibiotic-resistant isoleucyl-tRNA synthetase (ileS);  antibiotic target alteration;  mupirocin-like antibiotic;  mupirocin; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_name with mupirocin-like antibiotic
UPDATED category_aro_cvterm_id with 45733
UPDATED category_aro_accession with 3007151
UPDATED category_aro_class_name with Drug Class
UPDATED category_aro_description with A group of antibiotics including mupirocin and similar mixtures (such as those including pseudomonic acid A).
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2270	UPDATE	Staphylococcus aureus mupA conferring resistance to mupirocin	 antibiotic-resistant isoleucyl-tRNA synthetase (ileS);  antibiotic target alteration;  mupirocin-like antibiotic;  mupirocin; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_name with mupirocin-like antibiotic
UPDATED category_aro_cvterm_id with 45733
UPDATED category_aro_accession with 3007151
UPDATED category_aro_class_name with Drug Class
UPDATED category_aro_description with A group of antibiotics including mupirocin and similar mixtures (such as those including pseudomonic acid A).
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2272	UPDATE	Enterococcus faecalis cls with mutation conferring resistance to daptomycin	 peptide antibiotic;  antibiotic target alteration;  daptomycin resistant cls;  daptomycin; 	model_description; model_param	"UPDATED model_description with Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
UPDATED param_description with A subtype of the insertion mutation detection model parameter is used when a set of insertion mutations are reported in a peptide sequence format, encoded as [+][AAs][position range], for example +D345 or +MPL110-112.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
UPDATED param_description with A subtype of the deletion mutation detection model parameter used when a set of deletion mutations are reported in a peptide sequence format, encoded as [-][AAs][position range], for example -K527 or -QN517-518.
"
1863	UPDATE	VIM-3	 penam;  antibiotic inactivation;  penem;  carbapenem;  cephalosporin;  cephamycin;  VIM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2279	UPDATE	Listeria monocytogenes mprF	 peptide antibiotic;  antibiotic target alteration;  defensin resistant mprF;  defensin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2278	UPDATE	Bifidobacterium bifidum ileS conferring resistance to mupirocin	 antibiotic-resistant isoleucyl-tRNA synthetase (ileS);  antibiotic target alteration;  mupirocin-like antibiotic;  mupirocin; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_name with mupirocin-like antibiotic
UPDATED category_aro_cvterm_id with 45733
UPDATED category_aro_accession with 3007151
UPDATED category_aro_class_name with Drug Class
UPDATED category_aro_description with A group of antibiotics including mupirocin and similar mixtures (such as those including pseudomonic acid A).
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4300	UPDATE	ADC-235	 antibiotic inactivation;  cephalosporin;  ADC beta-lactamases pending classification for carbapenemase activity; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
708	UPDATE	CTX-M-49	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2154	UPDATE	Borreliella burgdorferi 16S rRNA mutation conferring resistance to spectinomycin	 antibiotic target alteration;  aminoglycoside antibiotic;  spectinomycin;  16s rRNA with mutation conferring resistance to aminoglycoside antibiotics; 	model_description; model_param	"UPDATED model_description with Ribosomal RNA (rRNA) Gene Variant Models (RVM) are similar to Protein Variant Models (PVM), i.e. detect  sequences based on their similarity to a curated reference sequence and secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles, except RVMs are designed to detect AMR acquired via mutation of genes encoding ribosomal RNAs (rRNA). RVMs include a rRNA reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTN bit-score above the curated BLASTN cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTN bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
UPDATED param_description with The BLASTN bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
"
1248	UPDATE	H-NS	 penam;  antibiotic efflux;  major facilitator superfamily (MFS) antibiotic efflux pump;  resistance-nodulation-cell division (RND) antibiotic efflux pump;  protein(s) and two-component regulatory system modulating antibiotic efflux;  norfloxacin;  macrolide antibiotic;  efflux pump complex or subunit conferring antibiotic resistance;  cephalosporin;  cephamycin;  oxacillin;  ciprofloxacin;  tetracycline antibiotic;  cloxacillin;  fluoroquinolone antibiotic;  tetracycline;  erythromycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1071	UPDATE	DHA-22	 antibiotic inactivation;  cephalosporin;  cephamycin;  DHA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4318	UPDATE	ADC-252	 antibiotic inactivation;  cephalosporin;  ADC beta-lactamases pending classification for carbapenemase activity; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5541	UPDATE	PDC-411	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
179	UPDATE	QnrA5	 sparfloxacin;  norfloxacin;  quinolone resistance protein (qnr);  gatifloxacin;  levofloxacin;  antibiotic target protection;  ciprofloxacin;  fluoroquinolone antibiotic;  nalidixic acid;  moxifloxacin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
178	UPDATE	vanH gene in vanA cluster	 vanH;  glycopeptide resistance gene cluster;  teicoplanin;  glycopeptide antibiotic;  antibiotic target alteration;  vancomycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_value with 200
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
177	UPDATE	IMP-51	 penam;  antibiotic inactivation;  penem;  carbapenem;  cephalosporin;  IMP beta-lactamase;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
176	UPDATE	CMY-25	 antibiotic inactivation;  CMY beta-lactamase;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
175	UPDATE	CTX-M-24	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
174	UPDATE	CfxA2	 antibiotic inactivation;  cephamycin;  CfxA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
173	UPDATE	arr-4	 antibiotic inactivation;  rifampin;  rifapentine;  rifabutin;  rifampin ADP-ribosyltransferase (Arr);  rifaximin;  rifamycin antibiotic; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
172	UPDATE	OprN	 antibiotic efflux;  resistance-nodulation-cell division (RND) antibiotic efflux pump;  norfloxacin;  trimethoprim;  efflux pump complex or subunit conferring antibiotic resistance;  diaminopyrimidine antibiotic;  ciprofloxacin;  fluoroquinolone antibiotic;  phenicol antibiotic;  chloramphenicol; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
171	UPDATE	TEM-78	 penam;  antibiotic inactivation;  penem;  cephalosporin;  monobactam;  ampicillin;  TEM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
170	UPDATE	IMP-19	 penam;  antibiotic inactivation;  penem;  carbapenem;  cephalosporin;  IMP beta-lactamase;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2051	UPDATE	dfrA15	 trimethoprim;  diaminopyrimidine antibiotic;  trimethoprim resistant dihydrofolate reductase dfr;  antibiotic target replacement; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2050	UPDATE	OXA-331	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2053	UPDATE	dfrA7	 trimethoprim;  diaminopyrimidine antibiotic;  trimethoprim resistant dihydrofolate reductase dfr;  antibiotic target replacement; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2052	UPDATE	APH(3'')-Ic	 antibiotic inactivation;  APH(3'');  streptomycin;  aminoglycoside antibiotic; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2055	UPDATE	LRA-3	 penam;  antibiotic inactivation;  subclass B3 LRA beta-lactamase;  cephalosporin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2054	UPDATE	msrC	 quinupristin;  macrolide antibiotic;  streptogramin B antibiotic;  msr-type ABC-F protein;  antibiotic target protection;  streptogramin antibiotic;  erythromycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2057	UPDATE	SHV-179	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  SHV beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4829	UPDATE	OXA-489	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4534	UPDATE	CTX-M-205	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2058	UPDATE	pp-flo	 antibiotic efflux;  major facilitator superfamily (MFS) antibiotic efflux pump;  efflux pump complex or subunit conferring antibiotic resistance;  florfenicol;  phenicol antibiotic;  chloramphenicol; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4824	UPDATE	OXA-159	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4537	UPDATE	CTX-M-208	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4530	UPDATE	CTX-M-201	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4823	UPDATE	OXA-114x	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4532	UPDATE	CTX-M-203	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4821	UPDATE	OXA-114v	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
655	UPDATE	OXA-243	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4802	UPDATE	OXA-114b	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
652	UPDATE	tcr3	 tetracycline antibiotic;  efflux pump complex or subunit conferring antibiotic resistance;  major facilitator superfamily (MFS) antibiotic efflux pump;  tetracycline;  antibiotic efflux; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4856	UPDATE	OXA-521	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
653	UPDATE	AAC(3)-VIIa	 antibiotic inactivation;  AAC(3);  aminoglycoside antibiotic;  paromomycin; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with paromomycin
UPDATED category_aro_cvterm_id with 37001
UPDATED category_aro_accession with 3000657
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with An aminoglycoside antibiotic used for the treatment of parasitic infections. It is similar to neomycin sharing a similar spectrum of activity, but its hydroxyl group at the 6'-position instead of an amino group makes it resistant to AAC(6') modifying enzymes.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1367	UPDATE	oleD	 antibiotic inactivation;  ole glycosyltransferase;  macrolide antibiotic;  tylosin;  erythromycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
650	UPDATE	aadA	 antibiotic inactivation;  aminoglycoside antibiotic;  ANT(3'');  streptomycin;  spectinomycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1505	UPDATE	SAT-4	 streptothricin acetyltransferase (SAT);  streptothricin;  antibiotic inactivation;  nucleoside antibiotic; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
670	UPDATE	IND-3	 carbapenem;  antibiotic inactivation;  IND beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3526	UPDATE	OXA-459	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3527	UPDATE	OXA-460	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3524	UPDATE	OXA-457	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3525	UPDATE	OXA-458	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3522	UPDATE	OXA-453	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3523	UPDATE	OXA-455	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3520	UPDATE	OXA-451	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3521	UPDATE	OXA-452	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4916	UPDATE	OXA-590	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3528	UPDATE	OXA-461	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3529	UPDATE	OXA-464	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4655	UPDATE	GOB-42	 carbapenem;  penam;  GOB beta-lactamase;  antibiotic inactivation;  cephalosporin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3254	UPDATE	NDM-11	 antibiotic inactivation;  penam;  carbapenem;  cephalosporin;  cephamycin;  NDM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4654	UPDATE	GOB-41	 carbapenem;  penam;  GOB beta-lactamase;  antibiotic inactivation;  cephalosporin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
314	UPDATE	TEM-176	 penam;  antibiotic inactivation;  penem;  cephalosporin;  monobactam;  ampicillin;  TEM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3543	UPDATE	OXA-482	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1091	UPDATE	IMP-6	 penam;  antibiotic inactivation;  penem;  carbapenem;  cephalosporin;  IMP beta-lactamase;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4657	UPDATE	GOB-44	 carbapenem;  penam;  GOB beta-lactamase;  antibiotic inactivation;  cephalosporin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
945	UPDATE	tet(40)	 tetracycline antibiotic;  efflux pump complex or subunit conferring antibiotic resistance;  major facilitator superfamily (MFS) antibiotic efflux pump;  tetracycline;  antibiotic efflux; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1977	UPDATE	AAC(6')-Ik	 antibiotic inactivation;  AAC(6');  kanamycin A;  amikacin;  aminoglycoside antibiotic;  tobramycin; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with kanamycin A
UPDATED category_aro_cvterm_id with 35966
UPDATED category_aro_accession with 0000049
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.
UPDATED category_aro_name with amikacin
UPDATED category_aro_cvterm_id with 35932
UPDATED category_aro_accession with 0000013
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.
UPDATED category_aro_name with tobramycin
UPDATED category_aro_cvterm_id with 35969
UPDATED category_aro_accession with 0000052
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4656	UPDATE	GOB-43	 carbapenem;  penam;  GOB beta-lactamase;  antibiotic inactivation;  cephalosporin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4539	UPDATE	CTX-M-210	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2697	UPDATE	EdeQ	 antibiotic inactivation;  polyamine antibiotic;  Edeine acetyltransferase;  edeine B;  edeine F;  edeine D;  peptide antibiotic;  edeine A; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4651	UPDATE	GOB-38	 carbapenem;  penam;  GOB beta-lactamase;  antibiotic inactivation;  cephalosporin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2695	UPDATE	MexCD-OprJ with type B NfxB mutation	 penam;  antibiotic efflux;  resistance-nodulation-cell division (RND) antibiotic efflux pump;  ofloxacin;  trimethoprim;  aminocoumarin antibiotic;  novobiocin;  macrolide antibiotic;  phenicol antibiotic;  efflux pump complex or subunit conferring antibiotic resistance;  cephalosporin;  diaminopyrimidine antibiotic;  tetracycline antibiotic;  gentamicin C;  chloramphenicol;  aminoglycoside antibiotic;  fluoroquinolone antibiotic;  tetracycline;  erythromycin; 	model_description; model_param	"UPDATED model_description with Efflux Pump System Meta-Models (EPS) are dedicated to efflux complexes and their regulators, such as AcrAB-TolC. Using the efflux pump components parameter, this model type simply includes a list of detection models for each component of the complex. This model type is still under development and not currently supported by the Resistance Gene Identifier (RGI) software.
UPDATED param_description with Association of proteins within efflux protein complexes or regulatory networks are encoded by the efflux pump components parameter: model_id,model_id,model_id, etc.
"
2694	UPDATE	MexCD-OprJ with type A NfxB mutation	 penam;  antibiotic efflux;  resistance-nodulation-cell division (RND) antibiotic efflux pump;  ofloxacin;  trimethoprim;  aminocoumarin antibiotic;  novobiocin;  macrolide antibiotic;  efflux pump complex or subunit conferring antibiotic resistance;  cephalosporin;  diaminopyrimidine antibiotic;  tetracycline antibiotic;  fluoroquinolone antibiotic;  erythromycin;  phenicol antibiotic;  tetracycline;  chloramphenicol; 	model_description; model_param	"UPDATED model_description with Efflux Pump System Meta-Models (EPS) are dedicated to efflux complexes and their regulators, such as AcrAB-TolC. Using the efflux pump components parameter, this model type simply includes a list of detection models for each component of the complex. This model type is still under development and not currently supported by the Resistance Gene Identifier (RGI) software.
UPDATED param_description with Association of proteins within efflux protein complexes or regulatory networks are encoded by the efflux pump components parameter: model_id,model_id,model_id, etc.
"
2693	UPDATE	Type B NfxB	 penam;  antibiotic efflux;  resistance-nodulation-cell division (RND) antibiotic efflux pump;  protein(s) and two-component regulatory system modulating antibiotic efflux;  ofloxacin;  trimethoprim;  aminocoumarin antibiotic;  novobiocin;  macrolide antibiotic;  phenicol antibiotic;  efflux pump complex or subunit conferring antibiotic resistance;  cephalosporin;  diaminopyrimidine antibiotic;  tetracycline antibiotic;  gentamicin C;  chloramphenicol;  aminoglycoside antibiotic;  fluoroquinolone antibiotic;  tetracycline;  erythromycin; 	model_description; model_param	"UPDATED model_description with Protein Overexpression Models (POM) are similar to Protein Variant Models (PVM) in that they include a protein reference sequence, a curated BLASTP bitscore cut-off, and mapped resistance variants. Whereas PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, reporting only those with curated mutations conferring AMR, POMs are restricted to regulatory proteins and report both wild-type sequences and/or sequences with mutations leading to overexpression of efflux complexes. The former lead to efflux of antibiotics at basal levels, while the latter can confer clinical resistance. POMs include a protein reference sequence (often from wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Perfect RGI match is 100% identical to the wild-type reference protein sequence along its entire length, a Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value may or may not contain at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off may or may not contain at least one curated mutation from amongst the mapped resistance variants.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
"
1975	UPDATE	blt	 antibiotic efflux;  major facilitator superfamily (MFS) antibiotic efflux pump;  efflux pump complex or subunit conferring antibiotic resistance;  acriflavine;  fluoroquinolone antibiotic;  disinfecting agents and antiseptics; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2691	UPDATE	Type A NfxB	 penam;  antibiotic efflux;  resistance-nodulation-cell division (RND) antibiotic efflux pump;  protein(s) and two-component regulatory system modulating antibiotic efflux;  ofloxacin;  trimethoprim;  aminocoumarin antibiotic;  novobiocin;  macrolide antibiotic;  efflux pump complex or subunit conferring antibiotic resistance;  cephalosporin;  diaminopyrimidine antibiotic;  tetracycline antibiotic;  fluoroquinolone antibiotic;  erythromycin;  phenicol antibiotic;  tetracycline;  chloramphenicol; 	model_description; model_param	"UPDATED model_description with Protein Overexpression Models (POM) are similar to Protein Variant Models (PVM) in that they include a protein reference sequence, a curated BLASTP bitscore cut-off, and mapped resistance variants. Whereas PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, reporting only those with curated mutations conferring AMR, POMs are restricted to regulatory proteins and report both wild-type sequences and/or sequences with mutations leading to overexpression of efflux complexes. The former lead to efflux of antibiotics at basal levels, while the latter can confer clinical resistance. POMs include a protein reference sequence (often from wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Perfect RGI match is 100% identical to the wild-type reference protein sequence along its entire length, a Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value may or may not contain at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off may or may not contain at least one curated mutation from amongst the mapped resistance variants.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
"
4650	UPDATE	GOB-37	 carbapenem;  penam;  GOB beta-lactamase;  antibiotic inactivation;  cephalosporin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4653	UPDATE	GOB-40	 carbapenem;  penam;  GOB beta-lactamase;  antibiotic inactivation;  cephalosporin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1973	UPDATE	TEM-111	 penam;  antibiotic inactivation;  penem;  cephalosporin;  monobactam;  ampicillin;  TEM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4983	UPDATE	OXA-666	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4652	UPDATE	GOB-39	 carbapenem;  penam;  GOB beta-lactamase;  antibiotic inactivation;  cephalosporin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4661	UPDATE	GOB-49	 carbapenem;  penam;  GOB beta-lactamase;  antibiotic inactivation;  cephalosporin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1972	UPDATE	OXA-149	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1971	UPDATE	dfrB2	 trimethoprim;  diaminopyrimidine antibiotic;  trimethoprim resistant dihydrofolate reductase dfr;  antibiotic target replacement; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1970	UPDATE	SHV-44	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  SHV beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1362	UPDATE	IMP-31	 penam;  antibiotic inactivation;  penem;  carbapenem;  cephalosporin;  IMP beta-lactamase;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1968	UPDATE	SHV-189	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  SHV beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1969	UPDATE	tet(35)	 tetracycline antibiotic;  efflux pump complex or subunit conferring antibiotic resistance;  ATP-binding cassette (ABC) antibiotic efflux pump;  tetracycline;  antibiotic efflux; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1618	UPDATE	OXA-362	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1619	UPDATE	L1 beta-lactamase	 antibiotic inactivation;  cephalosporin;  L1 family beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1616	UPDATE	CTX-M-152	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1617	UPDATE	vanE	 glycopeptide antibiotic;  glycopeptide resistance gene cluster;  Van ligase;  vancomycin;  antibiotic target alteration; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with vancomycin
UPDATED category_aro_cvterm_id with 35947
UPDATED category_aro_accession with 0000028
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.
UPDATED param_value with 275
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1614	UPDATE	TEM-194	 penam;  antibiotic inactivation;  penem;  cephalosporin;  monobactam;  ampicillin;  TEM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1615	UPDATE	APH(2'')-IIa	 antibiotic inactivation;  kanamycin A;  gentamicin B;  aminoglycoside antibiotic;  plazomicin;  sisomicin;  arbekacin;  APH(2'');  netilmicin;  gentamicin C;  amikacin;  isepamicin;  tobramycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1612	UPDATE	ErmR	 streptogramin A antibiotic;  antibiotic target alteration;  virginiamycin S2;  vernamycin C;  pristinamycin IC;  patricin B;  patricin A;  oleandomycin;  ostreogrycin B3;  macrolide antibiotic;  telithromycin;  tylosin;  lincosamide antibiotic;  dirithromycin;  clarithromycin;  clindamycin;  dalfopristin;  pristinamycin IB;  quinupristin;  pristinamycin IA;  Erm 23S ribosomal RNA methyltransferase;  virginiamycin M1;  madumycin II;  griseoviridin;  streptogramin B antibiotic;  lincomycin;  streptogramin antibiotic;  roxithromycin;  spiramycin;  azithromycin;  erythromycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1613	UPDATE	CMY-38	 antibiotic inactivation;  CMY beta-lactamase;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1610	UPDATE	OXA-74	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1611	UPDATE	SME-4	 carbapenem;  antibiotic inactivation;  SME beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2063	UPDATE	blaR1	 penam;  antibiotic inactivation;  BlaZ beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1363	UPDATE	CARB-1	 penam;  antibiotic inactivation;  CARB beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2873	UPDATE	catV	 antibiotic inactivation;  phenicol antibiotic;  chloramphenicol acetyltransferase (CAT);  chloramphenicol; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2872	UPDATE	PDC-93	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2871	UPDATE	PDC-92	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2870	UPDATE	PDC-91	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2877	UPDATE	OXA-535	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2876	UPDATE	OXA-436	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2875	UPDATE	sul4	 sulfamethoxazole;  antibiotic target replacement;  sulfonamide resistant sul;  sulfonamide antibiotic; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with sulfamethoxazole
UPDATED category_aro_cvterm_id with 36468
UPDATED category_aro_accession with 3000329
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Sulfamethoxazole is a sulfonamide antibiotic usually taken with trimethoprim, a diaminopyrimidine antibiotic. Sulfamethoxazole inhibits dihydropteroate synthase, essential to tetrahydrofolic acid biosynthesis. This pathway generates compounds used in the synthesis of many amino acids and nucleotides.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2874	UPDATE	ACI-1	 penam;  antibiotic inactivation;  penem;  cephalosporin;  cefotaxime;  ceftazidime;  penicillin;  ticarcillin;  amoxicillin;  ACI beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
597	UPDATE	Klebsiella pneumoniae ramR mutants	 penam;  antibiotic efflux;  triclosan;  rifampin;  resistance-nodulation-cell division (RND) antibiotic efflux pump;  protein(s) and two-component regulatory system modulating antibiotic efflux;  efflux pump complex or subunit conferring antibiotic resistance;  antibiotic target alteration;  disinfecting agents and antiseptics;  tetracycline antibiotic;  cephalosporin;  cefalotin;  tigecycline;  glycylcycline;  ampicillin;  fluoroquinolone antibiotic;  rifamycin antibiotic;  phenicol antibiotic;  tetracycline;  chloramphenicol; 	model_description; model_param	"UPDATED model_description with Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
"
2878	UPDATE	almG	 peptide antibiotic;  antibiotic target alteration;  lipid A acyltransferase;  polymyxin B; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with polymyxin B
UPDATED category_aro_cvterm_id with 36593
UPDATED category_aro_accession with 3000454
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Polymyxin B is mixture of mostly polymyxins B1 and B2, mainly used for resistant gram-negative infections. They are polypeptides with cationic detergent action on cell membranes.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3355	UPDATE	catII from Escherichia coli K-12	 antibiotic inactivation;  phenicol antibiotic;  chloramphenicol acetyltransferase (CAT);  chloramphenicol; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3357	UPDATE	catA4	 antibiotic inactivation;  phenicol antibiotic;  chloramphenicol acetyltransferase (CAT);  chloramphenicol; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3356	UPDATE	OXA-296	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3351	UPDATE	Erm(O)-lrm	 Erm 23S ribosomal RNA methyltransferase;  macrolide antibiotic;  lincomycin;  antibiotic target alteration;  streptogramin antibiotic;  erythromycin;  tylosin;  lincosamide antibiotic; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with lincomycin
UPDATED category_aro_cvterm_id with 35964
UPDATED category_aro_accession with 0000046
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Lincomycin is a lincosamide antibiotic that comes from the actinomyces Streptomyces lincolnensis. It binds to the 23s portion of the 50S subunit of bacterial ribosomes and inhibit early elongation of peptide chain by inhibiting transpeptidase reaction.
UPDATED category_aro_name with tylosin
UPDATED category_aro_cvterm_id with 36284
UPDATED category_aro_accession with 3000145
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Tylosin is a 16-membered macrolide, naturally produced by Streptomyces fradiae. It interacts with the bacterial ribosome 50S subunit to inhibit protein synthesis.
UPDATED category_aro_name with erythromycin
UPDATED category_aro_cvterm_id with 35925
UPDATED category_aro_accession with 0000006
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure/function processes critical for life or replication are inhibited.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3353	UPDATE	Clostridioides difficile 23S rRNA with mutation conferring resistance to erythromycin and clindamycin	 23S rRNA with mutation conferring resistance to macrolide antibiotics;  erythromycin;  macrolide antibiotic;  antibiotic target alteration;  clindamycin;  lincosamide antibiotic; 	model_description; model_param	"UPDATED model_description with Ribosomal RNA (rRNA) Gene Variant Models (RVM) are similar to Protein Variant Models (PVM), i.e. detect  sequences based on their similarity to a curated reference sequence and secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles, except RVMs are designed to detect AMR acquired via mutation of genes encoding ribosomal RNAs (rRNA). RVMs include a rRNA reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTN bit-score above the curated BLASTN cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTN bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
UPDATED param_description with The BLASTN bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
"
1117	UPDATE	ErmD	 streptogramin A antibiotic;  antibiotic target alteration;  virginiamycin S2;  vernamycin C;  pristinamycin IC;  patricin B;  patricin A;  oleandomycin;  ostreogrycin B3;  macrolide antibiotic;  telithromycin;  tylosin;  lincosamide antibiotic;  dirithromycin;  clarithromycin;  clindamycin;  dalfopristin;  pristinamycin IB;  quinupristin;  pristinamycin IA;  Erm 23S ribosomal RNA methyltransferase;  virginiamycin M1;  madumycin II;  griseoviridin;  streptogramin B antibiotic;  lincomycin;  streptogramin antibiotic;  roxithromycin;  spiramycin;  azithromycin;  erythromycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3359	UPDATE	Mef(En2)	 efflux pump complex or subunit conferring antibiotic resistance;  major facilitator superfamily (MFS) antibiotic efflux pump;  macrolide antibiotic;  antibiotic efflux; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3358	UPDATE	catA8	 antibiotic inactivation;  phenicol antibiotic;  chloramphenicol acetyltransferase (CAT);  chloramphenicol; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5449	UPDATE	PDC-319	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5448	UPDATE	PDC-318	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1181	UPDATE	cmeA	 antibiotic efflux;  resistance-nodulation-cell division (RND) antibiotic efflux pump;  macrolide antibiotic;  cefotaxime;  efflux pump complex or subunit conferring antibiotic resistance;  cephalosporin;  fusidane antibiotic;  fusidic acid;  fluoroquinolone antibiotic;  erythromycin; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_name with fusidane antibiotic
UPDATED category_aro_cvterm_id with 45735
UPDATED category_aro_accession with 3007153
UPDATED category_aro_class_name with Drug Class
UPDATED category_aro_description with A group of antibiotics possessing steroid rings or steroid-like structures.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1366	UPDATE	cmx	 antibiotic efflux;  efflux pump complex or subunit conferring antibiotic resistance;  major facilitator superfamily (MFS) antibiotic efflux pump;  phenicol antibiotic;  chloramphenicol; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5443	UPDATE	PDC-312	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5442	UPDATE	PDC-311	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5441	UPDATE	PDC-310	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5440	UPDATE	PDC-31	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5447	UPDATE	PDC-317	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5446	UPDATE	PDC-316	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5445	UPDATE	PDC-315	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5444	UPDATE	PDC-314	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1768	UPDATE	CTX-M-144	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1769	UPDATE	CTX-M-115	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1361	UPDATE	OXA-223	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1762	UPDATE	aadA16	 antibiotic inactivation;  aminoglycoside antibiotic;  ANT(3'');  streptomycin;  spectinomycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1763	UPDATE	NDM-2	 antibiotic inactivation;  penam;  carbapenem;  cephalosporin;  cephamycin;  NDM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1760	UPDATE	QnrB35	 sparfloxacin;  norfloxacin;  quinolone resistance protein (qnr);  gatifloxacin;  levofloxacin;  antibiotic target protection;  ciprofloxacin;  fluoroquinolone antibiotic;  nalidixic acid;  moxifloxacin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1761	UPDATE	OXA-351	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1766	UPDATE	VIM-14	 penam;  antibiotic inactivation;  penem;  carbapenem;  cephalosporin;  cephamycin;  VIM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1767	UPDATE	OKP-A-16	 penam;  antibiotic inactivation;  OKP beta-lactamase;  cephalosporin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1764	UPDATE	OXA-97	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1765	UPDATE	OXA-56	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1142	UPDATE	dfrA17	 trimethoprim;  diaminopyrimidine antibiotic;  trimethoprim resistant dihydrofolate reductase dfr;  antibiotic target replacement; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1143	UPDATE	OXA-7	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1140	UPDATE	CMY-86	 antibiotic inactivation;  CMY beta-lactamase;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1141	UPDATE	OXA-169	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1146	UPDATE	TEM-156	 penam;  antibiotic inactivation;  penem;  cephalosporin;  monobactam;  ampicillin;  TEM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1147	UPDATE	CMY-63	 antibiotic inactivation;  CMY beta-lactamase;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1144	UPDATE	vgbB	 virginiamycin S2;  pristinamycin IB;  quinupristin;  pristinamycin IC;  patricin B;  patricin A;  ostreogrycin B3;  vernamycin C;  streptogramin B antibiotic;  pristinamycin IA;  antibiotic inactivation;  streptogramin antibiotic;  streptogramin vgb lyase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1145	UPDATE	CTX-M-124	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1148	UPDATE	OXA-363	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1149	UPDATE	AER-1	 AER beta-lactamase;  penam;  antibiotic inactivation; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
769	UPDATE	KPC-11	 antibiotic inactivation;  penam;  carbapenem;  cephalosporin;  monobactam;  KPC beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5508	UPDATE	PDC-378	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5509	UPDATE	PDC-379	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5506	UPDATE	PDC-375	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5507	UPDATE	PDC-377	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5504	UPDATE	PDC-373	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5505	UPDATE	PDC-374	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5502	UPDATE	PDC-371	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5503	UPDATE	PDC-372	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5500	UPDATE	PDC-37	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5501	UPDATE	PDC-370	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
692	UPDATE	TEM-159	 penam;  antibiotic inactivation;  penem;  cephalosporin;  monobactam;  ampicillin;  TEM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
693	UPDATE	OXA-22	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1544	UPDATE	dfrE	 trimethoprim;  diaminopyrimidine antibiotic;  trimethoprim resistant dihydrofolate reductase dfr;  antibiotic target replacement; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1545	UPDATE	Escherichia coli gyrA conferring resistance to fluoroquinolones	 grepafloxacin;  trovafloxacin;  ofloxacin;  norfloxacin;  nalidixic acid;  lomefloxacin;  gatifloxacin;  fluoroquinolone resistant gyrA;  levofloxacin;  sparfloxacin;  antibiotic target alteration;  enoxacin;  ciprofloxacin;  pefloxacin;  fluoroquinolone antibiotic;  moxifloxacin; 	model_description; model_param	"UPDATED model_description with Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
UPDATED param_description with A set of nucleotide or amino acid substitutions that are all required to confer resistance to an antibiotic drug or drug class, encoded as: [wild-type 1][position 1][mutation 1],[wild-type 2][position 2][mutation 2], etc. For example, D63Y,T142K.
"
696	UPDATE	cfrA	 dalfopristin;  thiamphenicol;  oxazolidinone antibiotic;  virginiamycin M1;  pleuromutilin antibiotic;  tiamulin;  madumycin II;  griseoviridin;  streptogramin A antibiotic;  lincomycin;  streptogramin antibiotic;  antibiotic target alteration;  lincosamide antibiotic;  azidamfenicol;  clindamycin;  phenicol antibiotic;  Cfr 23S ribosomal RNA methyltransferase;  chloramphenicol; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
697	UPDATE	Erm(42)	 Erm 23S ribosomal RNA methyltransferase;  erythromycin;  macrolide antibiotic;  antibiotic target alteration;  streptogramin antibiotic;  clindamycin;  lincosamide antibiotic; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with clindamycin
UPDATED category_aro_cvterm_id with 35983
UPDATED category_aro_accession with 0000066
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Clindamycin is a lincosamide antibiotic that blocks A-site aminoacyl-tRNA binding. It is usually used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria.
UPDATED category_aro_name with erythromycin
UPDATED category_aro_cvterm_id with 35925
UPDATED category_aro_accession with 0000006
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure/function processes critical for life or replication are inhibited.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
694	UPDATE	CTX-M-40	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
695	UPDATE	CMY-66	 antibiotic inactivation;  CMY beta-lactamase;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
698	UPDATE	TEM-205	 penam;  antibiotic inactivation;  penem;  cephalosporin;  monobactam;  ampicillin;  TEM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
699	UPDATE	QnrS9	 sparfloxacin;  norfloxacin;  quinolone resistance protein (qnr);  gatifloxacin;  levofloxacin;  antibiotic target protection;  ciprofloxacin;  fluoroquinolone antibiotic;  nalidixic acid;  moxifloxacin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1548	UPDATE	APH(3')-Vb	 antibiotic inactivation;  aminoglycoside antibiotic;  paromomycin;  APH(3');  ribostamycin;  G418;  neomycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1549	UPDATE	ErmB	 streptogramin A antibiotic;  antibiotic target alteration;  virginiamycin S2;  vernamycin C;  pristinamycin IC;  patricin B;  patricin A;  oleandomycin;  ostreogrycin B3;  macrolide antibiotic;  telithromycin;  tylosin;  lincosamide antibiotic;  dirithromycin;  clarithromycin;  clindamycin;  dalfopristin;  pristinamycin IB;  quinupristin;  pristinamycin IA;  Erm 23S ribosomal RNA methyltransferase;  virginiamycin M1;  madumycin II;  griseoviridin;  streptogramin B antibiotic;  lincomycin;  streptogramin antibiotic;  roxithromycin;  spiramycin;  azithromycin;  erythromycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
542	UPDATE	adeH	 antibiotic efflux;  resistance-nodulation-cell division (RND) antibiotic efflux pump;  efflux pump complex or subunit conferring antibiotic resistance;  tetracycline antibiotic;  fluoroquinolone antibiotic;  tetracycline; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
543	UPDATE	TEM-106	 penam;  antibiotic inactivation;  penem;  cephalosporin;  monobactam;  ampicillin;  TEM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
540	UPDATE	emrY	 tetracycline antibiotic;  efflux pump complex or subunit conferring antibiotic resistance;  major facilitator superfamily (MFS) antibiotic efflux pump;  tetracycline;  antibiotic efflux; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
541	UPDATE	TEM-133	 penam;  antibiotic inactivation;  penem;  cephalosporin;  monobactam;  ampicillin;  TEM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
546	UPDATE	TLA-1	 antibiotic inactivation;  monobactam;  fluoroquinolone antibiotic;  cephalosporin;  TLA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
547	UPDATE	arr-5	 antibiotic inactivation;  rifampin;  rifapentine;  rifabutin;  rifampin ADP-ribosyltransferase (Arr);  rifaximin;  rifamycin antibiotic; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
544	UPDATE	AAC(6')-Is	 antibiotic inactivation;  AAC(6');  kanamycin A;  amikacin;  aminoglycoside antibiotic;  tobramycin; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with kanamycin A
UPDATED category_aro_cvterm_id with 35966
UPDATED category_aro_accession with 0000049
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.
UPDATED category_aro_name with amikacin
UPDATED category_aro_cvterm_id with 35932
UPDATED category_aro_accession with 0000013
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.
UPDATED category_aro_name with tobramycin
UPDATED category_aro_cvterm_id with 35969
UPDATED category_aro_accession with 0000052
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
545	UPDATE	GES-22	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  GES beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1643	UPDATE	arnA	 antibiotic efflux;  ATP-binding cassette (ABC) antibiotic efflux pump;  polymyxin B;  protein(s) and two-component regulatory system modulating antibiotic efflux;  pmr phosphoethanolamine transferase;  macrolide antibiotic;  peptide antibiotic;  efflux pump complex or subunit conferring antibiotic resistance;  antibiotic target alteration;  resistance by absence;  erythromycin; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with antibiotic efflux
UPDATED category_aro_cvterm_id with 36001
UPDATED category_aro_accession with 0010000
UPDATED category_aro_class_name with Resistance Mechanism
UPDATED category_aro_description with Antibiotic resistance via the transport of antibiotics out of the cell.
UPDATED category_aro_name with ATP-binding cassette (ABC) antibiotic efflux pump
UPDATED category_aro_cvterm_id with 36002
UPDATED category_aro_accession with 0010001
UPDATED category_aro_class_name with AMR Gene Family
UPDATED category_aro_description with Directed pumping of antibiotic out of a cell to confer resistance. ATP-binding cassette (ABC) transporters are present in all cells of all organisms and use the energy of ATP binding/hydrolysis to transport substrates across cell membranes.
UPDATED category_aro_name with polymyxin B
UPDATED category_aro_cvterm_id with 36593
UPDATED category_aro_accession with 3000454
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Polymyxin B is mixture of mostly polymyxins B1 and B2, mainly used for resistant gram-negative infections. They are polypeptides with cationic detergent action on cell membranes.
UPDATED category_aro_name with protein(s) and two-component regulatory system modulating antibiotic efflux
UPDATED category_aro_cvterm_id with 36590
UPDATED category_aro_accession with 3000451
UPDATED category_aro_class_name with Efflux Regulator
UPDATED category_aro_description with Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.
UPDATED category_aro_name with macrolide antibiotic
UPDATED category_aro_cvterm_id with 35919
UPDATED category_aro_accession with 0000000
UPDATED category_aro_class_name with Drug Class
UPDATED category_aro_description with Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.
UPDATED category_aro_name with efflux pump complex or subunit conferring antibiotic resistance
UPDATED category_aro_cvterm_id with 36298
UPDATED category_aro_accession with 3000159
UPDATED category_aro_class_name with Efflux Component
UPDATED category_aro_description with Efflux proteins that pump antibiotic out of a cell to confer resistance.
UPDATED category_aro_name with resistance by absence
UPDATED category_aro_cvterm_id with 40429
UPDATED category_aro_accession with 3003764
UPDATED category_aro_class_name with Resistance Mechanism
UPDATED category_aro_description with Mechanism of antibiotic resistance conferred by deletion of gene (usually a porin).
UPDATED category_aro_name with erythromycin
UPDATED category_aro_cvterm_id with 35925
UPDATED category_aro_accession with 0000006
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure/function processes critical for life or replication are inhibited.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
548	UPDATE	QnrB3	 sparfloxacin;  norfloxacin;  quinolone resistance protein (qnr);  gatifloxacin;  levofloxacin;  antibiotic target protection;  ciprofloxacin;  fluoroquinolone antibiotic;  nalidixic acid;  moxifloxacin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
549	UPDATE	TEM-107	 penam;  antibiotic inactivation;  penem;  cephalosporin;  monobactam;  ampicillin;  TEM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
760	UPDATE	TEM-6	 penam;  antibiotic inactivation;  penem;  cephalosporin;  monobactam;  ampicillin;  TEM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
761	UPDATE	GES-13	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  GES beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
766	UPDATE	SHV-102	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  SHV beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2064	UPDATE	TEM-196	 penam;  antibiotic inactivation;  penem;  cephalosporin;  monobactam;  ampicillin;  TEM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
767	UPDATE	OXA-207	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5552	UPDATE	PDC-422	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
764	UPDATE	FOX-2	 antibiotic inactivation;  cephamycin;  cephalosporin;  FOX beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
765	UPDATE	QnrB7	 sparfloxacin;  norfloxacin;  quinolone resistance protein (qnr);  gatifloxacin;  levofloxacin;  antibiotic target protection;  ciprofloxacin;  fluoroquinolone antibiotic;  nalidixic acid;  moxifloxacin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5137	UPDATE	OXA-836	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5476	UPDATE	PDC-347	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5618	UPDATE	PER-15	 penam;  antibiotic inactivation;  penem;  carbapenem;  cephalosporin;  PER beta-lactamase;  monobactam; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5619	UPDATE	PER-16	 penam;  antibiotic inactivation;  penem;  carbapenem;  cephalosporin;  PER beta-lactamase;  monobactam; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4631	UPDATE	GMB-1	 carbapenem;  GMB beta-lactamase;  antibiotic inactivation; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
17	UPDATE	tet(45)	 tetracycline antibiotic;  efflux pump complex or subunit conferring antibiotic resistance;  major facilitator superfamily (MFS) antibiotic efflux pump;  tetracycline;  antibiotic efflux; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5477	UPDATE	PDC-348	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5612	UPDATE	PDC-99	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5613	UPDATE	PER-10	 penam;  antibiotic inactivation;  penem;  carbapenem;  cephalosporin;  PER beta-lactamase;  monobactam; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5610	UPDATE	PDC-97	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5611	UPDATE	PDC-98	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5616	UPDATE	PER-13	 penam;  antibiotic inactivation;  penem;  carbapenem;  cephalosporin;  PER beta-lactamase;  monobactam; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5617	UPDATE	PER-14	 penam;  antibiotic inactivation;  penem;  carbapenem;  cephalosporin;  PER beta-lactamase;  monobactam; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5614	UPDATE	PER-11	 penam;  antibiotic inactivation;  penem;  carbapenem;  cephalosporin;  PER beta-lactamase;  monobactam; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5615	UPDATE	PER-12	 penam;  antibiotic inactivation;  penem;  carbapenem;  cephalosporin;  PER beta-lactamase;  monobactam; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
414	UPDATE	OXA-377	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
415	UPDATE	TEM-33	 penam;  antibiotic inactivation;  penem;  cephalosporin;  monobactam;  ampicillin;  TEM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
416	UPDATE	OXA-204	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
417	UPDATE	QnrB6	 sparfloxacin;  norfloxacin;  quinolone resistance protein (qnr);  gatifloxacin;  levofloxacin;  antibiotic target protection;  ciprofloxacin;  fluoroquinolone antibiotic;  nalidixic acid;  moxifloxacin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1388	UPDATE	oleB	 Miscellaneous ABC-F subfamily ATP-binding cassette ribosomal protection proteins;  macrolide antibiotic;  oleandomycin;  antibiotic target protection; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
411	UPDATE	QnrB11	 sparfloxacin;  norfloxacin;  quinolone resistance protein (qnr);  gatifloxacin;  levofloxacin;  antibiotic target protection;  ciprofloxacin;  fluoroquinolone antibiotic;  nalidixic acid;  moxifloxacin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
412	UPDATE	OXA-117	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
413	UPDATE	OXA-144	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1384	UPDATE	OXA-382	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1385	UPDATE	mdsB	 penam;  antibiotic efflux;  resistance-nodulation-cell division (RND) antibiotic efflux pump;  penem;  carbapenem;  efflux pump complex or subunit conferring antibiotic resistance;  cephalosporin;  cephamycin;  monobactam;  phenicol antibiotic;  chloramphenicol; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1386	UPDATE	ANT(9)-Ia	 antibiotic inactivation;  aminoglycoside antibiotic;  spectinomycin;  ANT(9); 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1387	UPDATE	OXA-99	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1380	UPDATE	TEM-193	 penam;  antibiotic inactivation;  penem;  cephalosporin;  monobactam;  ampicillin;  TEM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
419	UPDATE	SLB-1	 penam;  antibiotic inactivation;  cephalosporin;  SHW beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1382	UPDATE	rmtG	 16S rRNA methyltransferase (G1405);  arbekacin;  antibiotic target alteration;  amikacin;  aminoglycoside antibiotic;  gentamicin A;  tobramycin; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with arbekacin
UPDATED category_aro_cvterm_id with 36998
UPDATED category_aro_accession with 3000654
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.
UPDATED category_aro_name with amikacin
UPDATED category_aro_cvterm_id with 35932
UPDATED category_aro_accession with 0000013
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.
UPDATED category_aro_name with gentamicin A
UPDATED category_aro_cvterm_id with 40942
UPDATED category_aro_accession with 3004015
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Gentamicin A is part of a complex of broad spectrum aminoglycoside antibiotics. Gentamicin inhibits protein synthesis, resulting in bacterial cell death.
UPDATED category_aro_name with tobramycin
UPDATED category_aro_cvterm_id with 35969
UPDATED category_aro_accession with 0000052
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1383	UPDATE	IMI-4	 carbapenem;  antibiotic inactivation;  IMI beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3827	UPDATE	OXA-898	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3826	UPDATE	OXA-899	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3825	UPDATE	RanA	 efflux pump complex or subunit conferring antibiotic resistance;  ATP-binding cassette (ABC) antibiotic efflux pump;  aminoglycoside antibiotic;  antibiotic efflux; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3824	UPDATE	RanB	 efflux pump complex or subunit conferring antibiotic resistance;  ATP-binding cassette (ABC) antibiotic efflux pump;  aminoglycoside antibiotic;  antibiotic efflux; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3823	UPDATE	mef(D)	 efflux pump complex or subunit conferring antibiotic resistance;  major facilitator superfamily (MFS) antibiotic efflux pump;  macrolide antibiotic;  antibiotic efflux; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3822	UPDATE	msrH	 streptogramin antibiotic;  antibiotic target protection;  macrolide antibiotic;  msr-type ABC-F protein;  erythromycin; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with erythromycin
UPDATED category_aro_cvterm_id with 35925
UPDATED category_aro_accession with 0000006
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure/function processes critical for life or replication are inhibited.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3821	UPDATE	msrF	 streptogramin antibiotic;  antibiotic target protection;  macrolide antibiotic;  msr-type ABC-F protein;  erythromycin; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with erythromycin
UPDATED category_aro_cvterm_id with 35925
UPDATED category_aro_accession with 0000006
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure/function processes critical for life or replication are inhibited.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3820	UPDATE	AAC(3)-IIg	 antibiotic inactivation;  AAC(3);  aminoglycoside antibiotic;  gentamicin A; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with gentamicin A
UPDATED category_aro_cvterm_id with 40942
UPDATED category_aro_accession with 3004015
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Gentamicin A is part of a complex of broad spectrum aminoglycoside antibiotics. Gentamicin inhibits protein synthesis, resulting in bacterial cell death.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3327	UPDATE	AAC(2')-IIa	 antibiotic inactivation;  aminoglycoside antibiotic;  AAC(2');  kasugamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2769	UPDATE	MdtNOP	 antibiotic efflux;  major facilitator superfamily (MFS) antibiotic efflux pump;  efflux pump complex or subunit conferring antibiotic resistance;  puromycin;  acriflavine;  nucleoside antibiotic;  disinfecting agents and antiseptics; 	model_description; model_param	"UPDATED model_description with Efflux Pump System Meta-Models (EPS) are dedicated to efflux complexes and their regulators, such as AcrAB-TolC. Using the efflux pump components parameter, this model type simply includes a list of detection models for each component of the complex. This model type is still under development and not currently supported by the Resistance Gene Identifier (RGI) software.
UPDATED param_description with Association of proteins within efflux protein complexes or regulatory networks are encoded by the efflux pump components parameter: model_id,model_id,model_id, etc.
"
3829	UPDATE	mecC-type BlaZ	 penam;  antibiotic inactivation;  BlaZ beta-lactamase;  penicillin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3828	UPDATE	GPC-1	 carbapenem;  antibiotic inactivation;  GPC beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3583	UPDATE	FAR-1	 penam;  antibiotic inactivation;  FAR beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3584	UPDATE	FIM-1	 carbapenem;  antibiotic inactivation;  cephalosporin;  FIM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5006	UPDATE	OXA-694	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4282	UPDATE	ADC-217	 antibiotic inactivation;  cephalosporin;  ADC beta-lactamases pending classification for carbapenemase activity; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4283	UPDATE	ADC-218	 antibiotic inactivation;  cephalosporin;  ADC beta-lactamases pending classification for carbapenemase activity; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4280	UPDATE	ADC-215	 antibiotic inactivation;  cephalosporin;  ADC beta-lactamases pending classification for carbapenemase activity; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4281	UPDATE	ADC-216	 antibiotic inactivation;  cephalosporin;  ADC beta-lactamases pending classification for carbapenemase activity; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4286	UPDATE	ADC-221	 antibiotic inactivation;  cephalosporin;  ADC beta-lactamases pending classification for carbapenemase activity; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4287	UPDATE	ADC-222	 antibiotic inactivation;  cephalosporin;  ADC beta-lactamases pending classification for carbapenemase activity; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4284	UPDATE	ADC-219	 antibiotic inactivation;  cephalosporin;  ADC beta-lactamases pending classification for carbapenemase activity; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4285	UPDATE	ADC-220	 antibiotic inactivation;  cephalosporin;  ADC beta-lactamases pending classification for carbapenemase activity; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4288	UPDATE	ADC-223	 antibiotic inactivation;  cephalosporin;  ADC beta-lactamases pending classification for carbapenemase activity; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4289	UPDATE	ADC-224	 antibiotic inactivation;  cephalosporin;  ADC beta-lactamases pending classification for carbapenemase activity; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3588	UPDATE	FONA-4	 penam;  antibiotic inactivation;  FONA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5744	UPDATE	msr(I)	 streptogramin antibiotic;  macrolide antibiotic;  msr-type ABC-F protein;  antibiotic target protection; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
368	UPDATE	CARB-14	 penam;  antibiotic inactivation;  CARB beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
369	UPDATE	SHV-15	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  SHV beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
366	UPDATE	Mycobacterium tuberculosis iniA mutant conferring resistance to ethambutol	 antibiotic efflux;  polyamine antibiotic;  Ethambutol resistant iniA;  efflux pump complex or subunit conferring antibiotic resistance;  ethambutol;  antibiotic target alteration; 	model_description; model_param	"UPDATED model_description with Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A subtype of the deletion mutation detection model parameter used when a set of deletion mutations are reported in a nucleotide sequence format, encoded as [-]nt[position]:[nucleotides], for example -nt25:T.
"
367	UPDATE	CTX-M-25	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
364	UPDATE	CMY-83	 antibiotic inactivation;  CMY beta-lactamase;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
365	UPDATE	TEM-122	 penam;  antibiotic inactivation;  penem;  cephalosporin;  monobactam;  ampicillin;  TEM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
362	UPDATE	CTX-M-151	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
363	UPDATE	TEM-155	 penam;  antibiotic inactivation;  penem;  cephalosporin;  monobactam;  ampicillin;  TEM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
360	UPDATE	AAC(6')-Iy	 AAC(6');  antibiotic inactivation;  aminoglycoside antibiotic; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
361	UPDATE	OXA-278	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5274	UPDATE	PDC-137	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2760	UPDATE	MexGHI-OpmD	 antibiotic efflux;  resistance-nodulation-cell division (RND) antibiotic efflux pump;  norfloxacin;  efflux pump complex or subunit conferring antibiotic resistance;  acriflavine;  tetracycline antibiotic;  fluoroquinolone antibiotic;  disinfecting agents and antiseptics;  tetracycline; 	model_description; model_param	"UPDATED model_description with Efflux Pump System Meta-Models (EPS) are dedicated to efflux complexes and their regulators, such as AcrAB-TolC. Using the efflux pump components parameter, this model type simply includes a list of detection models for each component of the complex. This model type is still under development and not currently supported by the Resistance Gene Identifier (RGI) software.
UPDATED param_description with Association of proteins within efflux protein complexes or regulatory networks are encoded by the efflux pump components parameter: model_id,model_id,model_id, etc.
"
5275	UPDATE	PDC-138	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1431	UPDATE	GES-15	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  GES beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5276	UPDATE	PDC-139	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
380	UPDATE	CTX-M-147	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
381	UPDATE	QnrS1	 sparfloxacin;  norfloxacin;  quinolone resistance protein (qnr);  gatifloxacin;  levofloxacin;  antibiotic target protection;  ciprofloxacin;  fluoroquinolone antibiotic;  nalidixic acid;  moxifloxacin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
382	UPDATE	QnrB61	 sparfloxacin;  norfloxacin;  quinolone resistance protein (qnr);  gatifloxacin;  levofloxacin;  antibiotic target protection;  ciprofloxacin;  fluoroquinolone antibiotic;  nalidixic acid;  moxifloxacin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
383	UPDATE	Pseudomonas mutant PhoQ conferring resistance to colistin	 antibiotic efflux;  ATP-binding cassette (ABC) antibiotic efflux pump;  colistin B;  polymyxin B;  protein(s) and two-component regulatory system modulating antibiotic efflux;  pmr phosphoethanolamine transferase;  colistin A;  macrolide antibiotic;  peptide antibiotic;  efflux pump complex or subunit conferring antibiotic resistance;  antibiotic target alteration;  resistance by absence;  erythromycin; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
UPDATED category_aro_name with resistance by absence
UPDATED category_aro_cvterm_id with 40429
UPDATED category_aro_accession with 3003764
UPDATED category_aro_class_name with Resistance Mechanism
UPDATED category_aro_description with Mechanism of antibiotic resistance conferred by deletion of gene (usually a porin).
UPDATED category_aro_name with polymyxin B
UPDATED category_aro_cvterm_id with 36593
UPDATED category_aro_accession with 3000454
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Polymyxin B is mixture of mostly polymyxins B1 and B2, mainly used for resistant gram-negative infections. They are polypeptides with cationic detergent action on cell membranes.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
"
384	UPDATE	APH(2'')-IVa	 antibiotic inactivation;  kanamycin A;  gentamicin B;  aminoglycoside antibiotic;  sisomicin;  arbekacin;  APH(2'');  netilmicin;  gentamicin C;  amikacin;  isepamicin;  gentamicin A;  tobramycin; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with gentamicin A
UPDATED category_aro_cvterm_id with 40942
UPDATED category_aro_accession with 3004015
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Gentamicin A is part of a complex of broad spectrum aminoglycoside antibiotics. Gentamicin inhibits protein synthesis, resulting in bacterial cell death.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
385	UPDATE	OXA-46	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
386	UPDATE	LEN-8	 penam;  LEN beta-lactamase;  antibiotic inactivation;  penem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
387	UPDATE	mdtA	 efflux pump complex or subunit conferring antibiotic resistance;  antibiotic efflux;  aminocoumarin antibiotic;  resistance-nodulation-cell division (RND) antibiotic efflux pump;  novobiocin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
388	UPDATE	QnrB71	 sparfloxacin;  norfloxacin;  quinolone resistance protein (qnr);  gatifloxacin;  levofloxacin;  antibiotic target protection;  ciprofloxacin;  fluoroquinolone antibiotic;  nalidixic acid;  moxifloxacin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
389	UPDATE	tet(W)	 chlortetracycline;  demeclocycline;  oxytetracycline;  tetracycline antibiotic;  tetracycline;  antibiotic target protection;  minocycline;  tetracycline-resistant ribosomal protection protein;  doxycycline; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5271	UPDATE	PDC-134	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4758	UPDATE	LUT-5	 antibiotic inactivation;  LUT beta-lactamase;  cephalosporin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4759	UPDATE	LUT-6	 antibiotic inactivation;  LUT beta-lactamase;  cephalosporin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2065	UPDATE	CMY-5	 antibiotic inactivation;  CMY beta-lactamase;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5272	UPDATE	PDC-135	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1369	UPDATE	QnrB69	 sparfloxacin;  norfloxacin;  quinolone resistance protein (qnr);  gatifloxacin;  levofloxacin;  antibiotic target protection;  ciprofloxacin;  fluoroquinolone antibiotic;  nalidixic acid;  moxifloxacin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4750	UPDATE	LHK-5	 carbapenem;  antibiotic inactivation;  cephalosporin;  LHK beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4751	UPDATE	LHK-6	 carbapenem;  antibiotic inactivation;  cephalosporin;  LHK beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4752	UPDATE	LRG-1	 antibiotic inactivation;  cephalosporin;  LRG beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4753	UPDATE	LUS-1	 LUS beta-lactamase;  carbapenem;  cephalosporin;  antibiotic inactivation; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4754	UPDATE	LUT-1	 antibiotic inactivation;  LUT beta-lactamase;  cephalosporin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4755	UPDATE	LUT-2	 antibiotic inactivation;  LUT beta-lactamase;  cephalosporin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4756	UPDATE	LUT-3	 antibiotic inactivation;  LUT beta-lactamase;  cephalosporin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4757	UPDATE	LUT-4	 antibiotic inactivation;  LUT beta-lactamase;  cephalosporin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1076	UPDATE	IMP-37	 penam;  antibiotic inactivation;  penem;  carbapenem;  cephalosporin;  IMP beta-lactamase;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1077	UPDATE	OXA-420	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1074	UPDATE	LEN-3	 penam;  LEN beta-lactamase;  antibiotic inactivation;  penem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
797	UPDATE	TEM-55	 penam;  antibiotic inactivation;  penem;  cephalosporin;  monobactam;  ampicillin;  TEM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3759	UPDATE	APH(3')-VIb	 antibiotic inactivation;  aminoglycoside antibiotic;  isepamicin;  paromomycin;  kanamycin A;  APH(3');  gentamicin B;  amikacin;  ribostamycin;  G418;  neomycin;  butirosin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3758	UPDATE	VMB-1	 carbapenem;  VMB beta-lactamase;  antibiotic inactivation; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1633	UPDATE	catQ	 antibiotic inactivation;  thiamphenicol;  chloramphenicol acetyltransferase (CAT);  azidamfenicol;  phenicol antibiotic;  chloramphenicol; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5376	UPDATE	PDC-238	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5553	UPDATE	PDC-423	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3751	UPDATE	TEM-181	 penam;  antibiotic inactivation;  penem;  cephalosporin;  monobactam;  ampicillin;  TEM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3750	UPDATE	tet(57)	 tetracycline antibiotic;  tetracycline-resistant ribosomal protection protein;  antibiotic target protection;  tetracycline; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with tetracycline
UPDATED category_aro_cvterm_id with 35968
UPDATED category_aro_accession with 0000051
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3753	UPDATE	TxR	 antibiotic efflux;  ATP-binding cassette (ABC) antibiotic efflux pump;  protein(s) and two-component regulatory system modulating antibiotic efflux;  efflux pump complex or subunit conferring antibiotic resistance;  tetracycline antibiotic;  tetracycline; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3755	UPDATE	qacEdelta1	 efflux pump complex or subunit conferring antibiotic resistance;  major facilitator superfamily (MFS) antibiotic efflux pump;  disinfecting agents and antiseptics;  antibiotic efflux; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3754	UPDATE	qacE	 efflux pump complex or subunit conferring antibiotic resistance;  major facilitator superfamily (MFS) antibiotic efflux pump;  disinfecting agents and antiseptics;  antibiotic efflux; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3757	UPDATE	IDC-2	 carbapenem;  antibiotic inactivation;  cephalosporin;  IDC beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3756	UPDATE	IDC-1	 carbapenem;  antibiotic inactivation;  cephalosporin;  IDC beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4633	UPDATE	GOB-20	 carbapenem;  penam;  GOB beta-lactamase;  antibiotic inactivation;  cephalosporin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2191	UPDATE	AAC(6')-Iaj	 AAC(6');  antibiotic inactivation;  aminoglycoside antibiotic; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
258	UPDATE	OXA-208	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2193	UPDATE	TriB	 efflux pump complex or subunit conferring antibiotic resistance;  triclosan;  antibiotic efflux;  resistance-nodulation-cell division (RND) antibiotic efflux pump;  disinfecting agents and antiseptics; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4637	UPDATE	GOB-24	 carbapenem;  penam;  GOB beta-lactamase;  antibiotic inactivation;  cephalosporin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2195	UPDATE	OpmH	 efflux pump complex or subunit conferring antibiotic resistance;  triclosan;  antibiotic efflux;  resistance-nodulation-cell division (RND) antibiotic efflux pump;  disinfecting agents and antiseptics; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2196	UPDATE	Pseudomonas aeruginosa gyrA conferring resistance to fluoroquinolones	 ofloxacin;  antibiotic target alteration;  fluoroquinolone resistant gyrA;  levofloxacin;  sparfloxacin;  ciprofloxacin;  pefloxacin;  fluoroquinolone antibiotic;  sitafloxacin; 	model_description; model_param	"UPDATED model_description with Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
UPDATED param_description with A set of nucleotide or amino acid substitutions that are all required to confer resistance to an antibiotic drug or drug class, encoded as: [wild-type 1][position 1][mutation 1],[wild-type 2][position 2][mutation 2], etc. For example, D63Y,T142K.
"
4634	UPDATE	GOB-21	 carbapenem;  penam;  GOB beta-lactamase;  antibiotic inactivation;  cephalosporin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2198	UPDATE	Pseudomonas aeruginosa parE conferring resistance to fluoroquinolones	 antibiotic target alteration;  fluoroquinolone resistant parE;  fluoroquinolone antibiotic;  ciprofloxacin; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
UPDATED category_aro_name with ciprofloxacin
UPDATED category_aro_cvterm_id with 35954
UPDATED category_aro_accession with 0000036
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
"
253	UPDATE	vanXY gene in vanG cluster	 glycopeptide antibiotic;  glycopeptide resistance gene cluster;  antibiotic target alteration;  vancomycin;  vanXY; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with vancomycin
UPDATED category_aro_cvterm_id with 35947
UPDATED category_aro_accession with 0000028
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.
UPDATED param_value with 125
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
250	UPDATE	Rhodococcus fascians cmr	 antibiotic efflux;  efflux pump complex or subunit conferring antibiotic resistance;  major facilitator superfamily (MFS) antibiotic efflux pump;  phenicol antibiotic;  chloramphenicol; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
251	UPDATE	APH(3')-VIIa	 antibiotic inactivation;  kanamycin A;  APH(3');  aminoglycoside antibiotic;  G418;  neomycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
256	UPDATE	CMY-21	 antibiotic inactivation;  CMY beta-lactamase;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
257	UPDATE	ACT-37	 antibiotic inactivation;  carbapenem;  penam;  ACT beta-lactamase;  cephalosporin;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
254	UPDATE	OXA-150	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
255	UPDATE	BRP(MBL)	 antibiotic inactivation;  bleomycin B2;  bleomycinic acid;  bleomycin A2;  Bleomycin resistant protein;  bleomycin;  glycopeptide antibiotic; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2200	UPDATE	APH(3')-VI	 antibiotic inactivation;  aminoglycoside antibiotic;  isepamicin;  paromomycin;  kanamycin A;  APH(3');  gentamicin B;  amikacin;  ribostamycin;  G418;  neomycin;  butirosin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2201	UPDATE	PvrR	 penam;  kanamycin A;  phenotypic variant regulator;  gentamicin A;  carbenicillin;  tetracycline antibiotic;  resistance by absence;  amikacin;  aminoglycoside antibiotic;  tetracycline;  tobramycin; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Knockout Models (PKM) reflect resistance by the absence of a gene product, most often deletion of a gene involved in antibiotic import, such as Vibrio cholerae OmpT. Like Protein Homolog Models (PHMs), PKMs include a reference sequence and a bitscore cut-off for detection using BLASTP but instead are designed to only report lack of detection under Perfect or Strict criteria. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff. This model type is still under development and not currently supported by the Resistance Gene Identifier (RGI) software.
UPDATED category_aro_name with penam
UPDATED category_aro_cvterm_id with 36017
UPDATED category_aro_accession with 3000008
UPDATED category_aro_class_name with Drug Class
UPDATED category_aro_description with Penams are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. This is the most defining feature of penicillins. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.
UPDATED category_aro_name with kanamycin A
UPDATED category_aro_cvterm_id with 35966
UPDATED category_aro_accession with 0000049
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.
UPDATED category_aro_name with tetracycline
UPDATED category_aro_cvterm_id with 35968
UPDATED category_aro_accession with 0000051
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.
UPDATED category_aro_name with carbenicillin
UPDATED category_aro_cvterm_id with 35961
UPDATED category_aro_accession with 0000043
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Carbenicillin is a semi-synthetic antibiotic belonging to the carboxypenicillin subgroup of the penicillins. It has gram-negative coverage which includes Pseudomonas aeruginosa but limited gram-positive coverage. The carboxypenicillins are susceptible to degradation by beta-lactamase enzymes. Carbenicillin antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.
UPDATED category_aro_name with tetracycline antibiotic
UPDATED category_aro_cvterm_id with 36189
UPDATED category_aro_accession with 3000050
UPDATED category_aro_class_name with Drug Class
UPDATED category_aro_description with These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.
UPDATED category_aro_name with amikacin
UPDATED category_aro_cvterm_id with 35932
UPDATED category_aro_accession with 0000013
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.
UPDATED category_aro_name with gentamicin A
UPDATED category_aro_cvterm_id with 40942
UPDATED category_aro_accession with 3004015
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Gentamicin A is part of a complex of broad spectrum aminoglycoside antibiotics. Gentamicin inhibits protein synthesis, resulting in bacterial cell death.
UPDATED category_aro_name with tobramycin
UPDATED category_aro_cvterm_id with 35969
UPDATED category_aro_accession with 0000052
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2202	UPDATE	AAC(3)-Ib/AAC(6')-Ib''	 antibiotic inactivation;  AAC(3);  AAC(6');  kanamycin A;  gentamicin C;  aminoglycoside antibiotic;  tobramycin; 	model_description; model_param; ARO_name	"UPDATED model_description with Protein Domain Meta-Models (PDMs) are dedicated to AMR fusion proteins, e.g. AAC(3)-Ib/AAC(6')-Ib''. The individual domains will have their own individual detection models (e.g. PHM, PVM, POM, etc.) while the PDM checks to see if all the component domiains of the fusion protein have a Strict or Perfect hit and are ordered correctly within the gene. This model type is still under development and not currently supported by the Resistance Gene Identifier (RGI) software.
UPDATED param_description with Spatial order of domains within a protein are encoded using the domain order parameter: [5' -> 3' position]:[cvterm_id],[5' -> 3' position]:[cvterm_id], etc.
UPDATED ARO_name with AAC(3)-Ib/AAC(6')-Ib'' fusion protein
"
2203	UPDATE	MCR-1.1	 peptide antibiotic;  MCR phosphoethanolamine transferase;  antibiotic target alteration;  colistin B;  colistin A; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2205	UPDATE	MexJ	 antibiotic efflux;  triclosan;  resistance-nodulation-cell division (RND) antibiotic efflux pump;  macrolide antibiotic;  efflux pump complex or subunit conferring antibiotic resistance;  tetracycline antibiotic;  disinfecting agents and antiseptics;  tetracycline;  erythromycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2206	UPDATE	MexK	 antibiotic efflux;  triclosan;  resistance-nodulation-cell division (RND) antibiotic efflux pump;  macrolide antibiotic;  efflux pump complex or subunit conferring antibiotic resistance;  tetracycline antibiotic;  disinfecting agents and antiseptics;  tetracycline;  erythromycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2207	UPDATE	MexV	 antibiotic efflux;  resistance-nodulation-cell division (RND) antibiotic efflux pump;  macrolide antibiotic;  disinfecting agents and antiseptics;  efflux pump complex or subunit conferring antibiotic resistance;  acriflavine;  tetracycline antibiotic;  fluoroquinolone antibiotic;  erythromycin;  phenicol antibiotic;  tetracycline;  chloramphenicol; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2208	UPDATE	MexW	 antibiotic efflux;  resistance-nodulation-cell division (RND) antibiotic efflux pump;  macrolide antibiotic;  disinfecting agents and antiseptics;  efflux pump complex or subunit conferring antibiotic resistance;  acriflavine;  tetracycline antibiotic;  fluoroquinolone antibiotic;  erythromycin;  phenicol antibiotic;  tetracycline;  chloramphenicol; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3985	UPDATE	TEM-210	 penam;  antibiotic inactivation;  penem;  cephalosporin;  monobactam;  ampicillin;  TEM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2428	UPDATE	farA	 antibiotic efflux;  major facilitator superfamily (MFS) antibiotic efflux pump;  linoleic acid;  efflux pump complex or subunit conferring antibiotic resistance;  antibacterial free fatty acids;  palmitic acid;  oleic acid; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2429	UPDATE	farB	 antibiotic efflux;  major facilitator superfamily (MFS) antibiotic efflux pump;  linoleic acid;  efflux pump complex or subunit conferring antibiotic resistance;  antibacterial free fatty acids;  palmitic acid;  oleic acid; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4812	UPDATE	OXA-114l	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2421	UPDATE	efrA	 antibiotic efflux;  ATP-binding cassette (ABC) antibiotic efflux pump;  rifampin;  macrolide antibiotic;  efflux pump complex or subunit conferring antibiotic resistance;  ciprofloxacin;  fluoroquinolone antibiotic;  rifamycin antibiotic;  erythromycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2422	UPDATE	efrB	 antibiotic efflux;  ATP-binding cassette (ABC) antibiotic efflux pump;  rifampin;  macrolide antibiotic;  efflux pump complex or subunit conferring antibiotic resistance;  ciprofloxacin;  fluoroquinolone antibiotic;  rifamycin antibiotic;  erythromycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2423	UPDATE	msbA	 nitroimidazole antibiotic;  metronidazole;  ATP-binding cassette (ABC) antibiotic efflux pump;  antibiotic efflux;  efflux pump complex or subunit conferring antibiotic resistance; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2424	UPDATE	YojI	 peptide antibiotic;  efflux pump complex or subunit conferring antibiotic resistance;  ATP-binding cassette (ABC) antibiotic efflux pump;  microcin J25;  antibiotic efflux; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2425	UPDATE	hmrM	 antibiotic efflux;  norfloxacin;  multidrug and toxic compound extrusion (MATE) transporter;  efflux pump complex or subunit conferring antibiotic resistance;  acriflavine;  fluoroquinolone antibiotic;  disinfecting agents and antiseptics; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2426	UPDATE	efmA	 antibiotic efflux;  major facilitator superfamily (MFS) antibiotic efflux pump;  macrolide antibiotic;  efflux pump complex or subunit conferring antibiotic resistance;  fluoroquinolone antibiotic;  erythromycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2427	UPDATE	efpA	 antibiotic efflux;  rifampin;  isoniazid;  efflux pump complex or subunit conferring antibiotic resistance;  major facilitator superfamily (MFS) antibiotic efflux pump;  isoniazid-like antibiotic;  rifamycin antibiotic; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_name with isoniazid-like antibiotic
UPDATED category_aro_cvterm_id with 45734
UPDATED category_aro_accession with 3007152
UPDATED category_aro_class_name with Drug Class
UPDATED category_aro_description with A group of antibiotics containing isoniazid and its derivatives.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4810	UPDATE	OXA-114j	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
168	UPDATE	VIM-17	 penam;  antibiotic inactivation;  penem;  carbapenem;  cephalosporin;  cephamycin;  VIM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
169	UPDATE	IMP-33	 penam;  antibiotic inactivation;  penem;  carbapenem;  cephalosporin;  IMP beta-lactamase;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
164	UPDATE	vanN	 glycopeptide antibiotic;  glycopeptide resistance gene cluster;  Van ligase;  vancomycin;  antibiotic target alteration; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with vancomycin
UPDATED category_aro_cvterm_id with 35947
UPDATED category_aro_accession with 0000028
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.
UPDATED param_value with 275
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
165	UPDATE	VIM-29	 penam;  antibiotic inactivation;  penem;  carbapenem;  cephalosporin;  cephamycin;  VIM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
268	UPDATE	CfxA6	 antibiotic inactivation;  cephamycin;  CfxA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
167	UPDATE	CMY-39	 antibiotic inactivation;  CMY beta-lactamase;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
160	UPDATE	OXA-236	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
161	UPDATE	SHV-56	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  SHV beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
162	UPDATE	KPC-8	 antibiotic inactivation;  penam;  carbapenem;  cephalosporin;  monobactam;  KPC beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
163	UPDATE	OXA-376	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4839	UPDATE	OXA-504	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4838	UPDATE	OXA-503	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4815	UPDATE	OXA-114p	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4529	UPDATE	CTX-M-200	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4528	UPDATE	CTX-M-199	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4527	UPDATE	CTX-M-198	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4526	UPDATE	CTX-M-197	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4525	UPDATE	CTX-M-196	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4524	UPDATE	CTX-M-195	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4523	UPDATE	CTX-M-194	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4522	UPDATE	CTX-M-193	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4521	UPDATE	CTX-M-192	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4520	UPDATE	CTX-M-191	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1843	UPDATE	rmtD	 16S rRNA methyltransferase (G1405);  arbekacin;  antibiotic target alteration;  amikacin;  aminoglycoside antibiotic;  gentamicin A;  tobramycin; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with arbekacin
UPDATED category_aro_cvterm_id with 36998
UPDATED category_aro_accession with 3000654
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.
UPDATED category_aro_name with amikacin
UPDATED category_aro_cvterm_id with 35932
UPDATED category_aro_accession with 0000013
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.
UPDATED category_aro_name with gentamicin A
UPDATED category_aro_cvterm_id with 40942
UPDATED category_aro_accession with 3004015
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Gentamicin A is part of a complex of broad spectrum aminoglycoside antibiotics. Gentamicin inhibits protein synthesis, resulting in bacterial cell death.
UPDATED category_aro_name with tobramycin
UPDATED category_aro_cvterm_id with 35969
UPDATED category_aro_accession with 0000052
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2518	UPDATE	tetB(58)	 tetracycline antibiotic;  efflux pump complex or subunit conferring antibiotic resistance;  major facilitator superfamily (MFS) antibiotic efflux pump;  tetracycline;  antibiotic efflux; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2519	UPDATE	LlmA 23S ribosomal RNA methyltransferase	 antibiotic target alteration;  clindamycin;  Llm 23S ribosomal RNA methyltransferase;  lincosamide antibiotic; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4423	UPDATE	CARB-38	 penam;  antibiotic inactivation;  CARB beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2066	UPDATE	Escherichia coli soxS with mutation conferring antibiotic resistance	 penem;  antibiotic target alteration;  tetracycline antibiotic;  antibiotic efflux;  ATP-binding cassette (ABC) antibiotic efflux pump;  major facilitator superfamily (MFS) antibiotic efflux pump;  resistance-nodulation-cell division (RND) antibiotic efflux pump;  norfloxacin;  reduced permeability to antibiotic;  carbapenem;  cephalosporin;  cefalotin;  ciprofloxacin;  disinfecting agents and antiseptics;  protein(s) and two-component regulatory system modulating antibiotic efflux;  rifampin;  ampicillin;  penam;  triclosan;  efflux pump complex or subunit conferring antibiotic resistance;  cephamycin;  tigecycline;  glycylcycline;  General Bacterial Porin with reduced permeability to beta-lactams;  monobactam;  fluoroquinolone antibiotic;  chloramphenicol;  phenicol antibiotic;  tetracycline;  rifamycin antibiotic; 	model_description; model_param	"UPDATED model_description with Protein Overexpression Models (POM) are similar to Protein Variant Models (PVM) in that they include a protein reference sequence, a curated BLASTP bitscore cut-off, and mapped resistance variants. Whereas PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, reporting only those with curated mutations conferring AMR, POMs are restricted to regulatory proteins and report both wild-type sequences and/or sequences with mutations leading to overexpression of efflux complexes. The former lead to efflux of antibiotics at basal levels, while the latter can confer clinical resistance. POMs include a protein reference sequence (often from wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Perfect RGI match is 100% identical to the wild-type reference protein sequence along its entire length, a Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value may or may not contain at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off may or may not contain at least one curated mutation from amongst the mapped resistance variants.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
"
2517	UPDATE	tetA(58)	 tetracycline antibiotic;  efflux pump complex or subunit conferring antibiotic resistance;  major facilitator superfamily (MFS) antibiotic efflux pump;  tetracycline;  antibiotic efflux; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
908	UPDATE	CTX-M-139	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2734	UPDATE	PmpM	 antibiotic efflux;  chlorhexidine;  multidrug and toxic compound extrusion (MATE) transporter;  efflux pump complex or subunit conferring antibiotic resistance;  benzalkonium chloride;  fluoroquinolone antibiotic;  aminoglycoside antibiotic;  disinfecting agents and antiseptics;  neomycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
909	UPDATE	OXA-5	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2731	UPDATE	MexJK-OpmH	 efflux pump complex or subunit conferring antibiotic resistance;  triclosan;  antibiotic efflux;  resistance-nodulation-cell division (RND) antibiotic efflux pump;  disinfecting agents and antiseptics; 	model_description; model_param	"UPDATED model_description with Efflux Pump System Meta-Models (EPS) are dedicated to efflux complexes and their regulators, such as AcrAB-TolC. Using the efflux pump components parameter, this model type simply includes a list of detection models for each component of the complex. This model type is still under development and not currently supported by the Resistance Gene Identifier (RGI) software.
UPDATED param_description with Association of proteins within efflux protein complexes or regulatory networks are encoded by the efflux pump components parameter: model_id,model_id,model_id, etc.
"
2732	UPDATE	MexVW-OprM	 antibiotic efflux;  resistance-nodulation-cell division (RND) antibiotic efflux pump;  macrolide antibiotic;  disinfecting agents and antiseptics;  efflux pump complex or subunit conferring antibiotic resistance;  acriflavine;  tetracycline antibiotic;  fluoroquinolone antibiotic;  erythromycin;  phenicol antibiotic;  tetracycline;  chloramphenicol; 	model_description; model_param	"UPDATED model_description with Efflux Pump System Meta-Models (EPS) are dedicated to efflux complexes and their regulators, such as AcrAB-TolC. Using the efflux pump components parameter, this model type simply includes a list of detection models for each component of the complex. This model type is still under development and not currently supported by the Resistance Gene Identifier (RGI) software.
UPDATED param_description with Association of proteins within efflux protein complexes or regulatory networks are encoded by the efflux pump components parameter: model_id,model_id,model_id, etc.
"
2733	UPDATE	TriABC-OpmH	 efflux pump complex or subunit conferring antibiotic resistance;  triclosan;  antibiotic efflux;  resistance-nodulation-cell division (RND) antibiotic efflux pump;  disinfecting agents and antiseptics; 	model_description; model_param	"UPDATED model_description with Efflux Pump System Meta-Models (EPS) are dedicated to efflux complexes and their regulators, such as AcrAB-TolC. Using the efflux pump components parameter, this model type simply includes a list of detection models for each component of the complex. This model type is still under development and not currently supported by the Resistance Gene Identifier (RGI) software.
UPDATED param_description with Association of proteins within efflux protein complexes or regulatory networks are encoded by the efflux pump components parameter: model_id,model_id,model_id, etc.
"
5296	UPDATE	PDC-158	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5297	UPDATE	PDC-159	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5294	UPDATE	PDC-156	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5295	UPDATE	PDC-157	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5292	UPDATE	PDC-154	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5293	UPDATE	PDC-155	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5290	UPDATE	PDC-152	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1846	UPDATE	CTX-M-91	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3531	UPDATE	OXA-466	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3530	UPDATE	OXA-465	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3533	UPDATE	OXA-471	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3532	UPDATE	OXA-470	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5058	UPDATE	OXA-749	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5059	UPDATE	OXA-750	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3537	UPDATE	OXA-475	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3536	UPDATE	OXA-474	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3539	UPDATE	OXA-477	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3538	UPDATE	OXA-476	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5056	UPDATE	OXA-747	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5057	UPDATE	OXA-748	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5050	UPDATE	OXA-741	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5051	UPDATE	OXA-742	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5052	UPDATE	OXA-743	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5053	UPDATE	OXA-744	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1814	UPDATE	AAC(6')-Ie-APH(2'')-Ia	 antibiotic inactivation;  kanamycin A;  gentamicin B;  AAC(6');  aminoglycoside antibiotic;  plazomicin;  sisomicin;  arbekacin;  APH(2'');  netilmicin;  gentamicin C;  amikacin;  isepamicin;  tobramycin; 	model_description; model_param; ARO_name; model_name	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED ARO_name with AAC(6')-Ie-APH(2'')-Ia bifunctional protein
UPDATED model_name with AAC(6')-Ie-APH(2'')-Ia bifunctional protein
"
1815	UPDATE	CTX-M-134	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1816	UPDATE	TEM-8	 penam;  antibiotic inactivation;  penem;  cephalosporin;  monobactam;  ampicillin;  TEM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1817	UPDATE	vgaB	 dalfopristin;  virginiamycin M1;  pleuromutilin antibiotic;  vga-type ABC-F protein;  streptogramin A antibiotic;  antibiotic target protection;  streptogramin antibiotic; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1810	UPDATE	VIM-15	 penam;  antibiotic inactivation;  penem;  carbapenem;  cephalosporin;  cephamycin;  VIM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1811	UPDATE	CARB-2	 penam;  antibiotic inactivation;  CARB beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1812	UPDATE	KHM-1	 penam;  antibiotic inactivation;  penem;  carbapenem;  cephalosporin;  cephamycin;  KHM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1813	UPDATE	MOX-4	 penam;  antibiotic inactivation;  MOX beta-lactamase;  cephamycin;  cephalosporin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1093	UPDATE	AAC(6')-31	 antibiotic inactivation;  kanamycin A;  aminoglycoside antibiotic;  AAC(6');  gentamicin A;  sisomicin;  netilmicin;  amikacin;  isepamicin;  neomycin;  tobramycin; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with sisomicin
UPDATED category_aro_cvterm_id with 35953
UPDATED category_aro_accession with 0000035
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.
UPDATED category_aro_name with neomycin
UPDATED category_aro_cvterm_id with 35924
UPDATED category_aro_accession with 0000005
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.
UPDATED category_aro_name with kanamycin A
UPDATED category_aro_cvterm_id with 35966
UPDATED category_aro_accession with 0000049
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.
UPDATED category_aro_name with netilmicin
UPDATED category_aro_cvterm_id with 35956
UPDATED category_aro_accession with 0000038
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.
UPDATED category_aro_name with amikacin
UPDATED category_aro_cvterm_id with 35932
UPDATED category_aro_accession with 0000013
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.
UPDATED category_aro_name with isepamicin
UPDATED category_aro_cvterm_id with 36996
UPDATED category_aro_accession with 3000652
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.
UPDATED category_aro_name with gentamicin A
UPDATED category_aro_cvterm_id with 40942
UPDATED category_aro_accession with 3004015
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Gentamicin A is part of a complex of broad spectrum aminoglycoside antibiotics. Gentamicin inhibits protein synthesis, resulting in bacterial cell death.
UPDATED category_aro_name with tobramycin
UPDATED category_aro_cvterm_id with 35969
UPDATED category_aro_accession with 0000052
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1818	UPDATE	GES-26	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  GES beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1819	UPDATE	TEM-3	 penam;  antibiotic inactivation;  penem;  cephalosporin;  monobactam;  ampicillin;  TEM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4912	UPDATE	OXA-586	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
674	UPDATE	OXA-15	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
300	UPDATE	AAC(6')-29a	 antibiotic inactivation;  AAC(6');  isepamicin;  kanamycin A;  amikacin;  aminoglycoside antibiotic;  tobramycin; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with kanamycin A
UPDATED category_aro_cvterm_id with 35966
UPDATED category_aro_accession with 0000049
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.
UPDATED category_aro_name with amikacin
UPDATED category_aro_cvterm_id with 35932
UPDATED category_aro_accession with 0000013
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.
UPDATED category_aro_name with isepamicin
UPDATED category_aro_cvterm_id with 36996
UPDATED category_aro_accession with 3000652
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.
UPDATED category_aro_name with tobramycin
UPDATED category_aro_cvterm_id with 35969
UPDATED category_aro_accession with 0000052
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
675	UPDATE	OXA-25	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
725	UPDATE	GES-11	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  GES beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
676	UPDATE	AAC(6')-Ih	 antibiotic inactivation;  AAC(6');  kanamycin A;  amikacin;  aminoglycoside antibiotic;  tobramycin; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with kanamycin A
UPDATED category_aro_cvterm_id with 35966
UPDATED category_aro_accession with 0000049
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.
UPDATED category_aro_name with amikacin
UPDATED category_aro_cvterm_id with 35932
UPDATED category_aro_accession with 0000013
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.
UPDATED category_aro_name with tobramycin
UPDATED category_aro_cvterm_id with 35969
UPDATED category_aro_accession with 0000052
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
677	UPDATE	OXA-171	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2008	UPDATE	SHV-145	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  SHV beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4332	UPDATE	ADC-54	 antibiotic inactivation;  cephalosporin;  ADC beta-lactamases pending classification for carbapenemase activity; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1087	UPDATE	OXA-253	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
671	UPDATE	CTX-M-137	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
672	UPDATE	CMY-27	 antibiotic inactivation;  CMY beta-lactamase;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
673	UPDATE	IMP-48	 penam;  antibiotic inactivation;  penem;  carbapenem;  cephalosporin;  IMP beta-lactamase;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1609	UPDATE	QnrC	 sparfloxacin;  norfloxacin;  quinolone resistance protein (qnr);  gatifloxacin;  levofloxacin;  antibiotic target protection;  ciprofloxacin;  fluoroquinolone antibiotic;  nalidixic acid;  moxifloxacin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1608	UPDATE	MexT	 antibiotic efflux;  resistance-nodulation-cell division (RND) antibiotic efflux pump;  protein(s) and two-component regulatory system modulating antibiotic efflux;  trimethoprim;  efflux pump complex or subunit conferring antibiotic resistance;  diaminopyrimidine antibiotic;  ciprofloxacin;  fluoroquinolone antibiotic;  phenicol antibiotic;  chloramphenicol; 	model_description; model_param	"UPDATED model_description with Protein Overexpression Models (POM) are similar to Protein Variant Models (PVM) in that they include a protein reference sequence, a curated BLASTP bitscore cut-off, and mapped resistance variants. Whereas PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, reporting only those with curated mutations conferring AMR, POMs are restricted to regulatory proteins and report both wild-type sequences and/or sequences with mutations leading to overexpression of efflux complexes. The former lead to efflux of antibiotics at basal levels, while the latter can confer clinical resistance. POMs include a protein reference sequence (often from wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Perfect RGI match is 100% identical to the wild-type reference protein sequence along its entire length, a Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value may or may not contain at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off may or may not contain at least one curated mutation from amongst the mapped resistance variants.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
"
1979	UPDATE	FosA4	 antibiotic inactivation;  fosfomycin thiol transferase;  phosphonic acid antibiotic; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
DELETED 35944
UPDATED category_aro_name with phosphonic acid antibiotic
UPDATED category_aro_cvterm_id with 45731
UPDATED category_aro_accession with 3007149
UPDATED category_aro_class_name with Drug Class
UPDATED category_aro_description with A group of antibiotics derived from phosphonic acids.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1978	UPDATE	OXA-200	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1601	UPDATE	LRA-1	 class A LRA beta-lactamase;  penam;  cephalosporin;  antibiotic inactivation; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1600	UPDATE	Pseudomonas mutant PhoP conferring resistance to colistin	 antibiotic efflux;  ATP-binding cassette (ABC) antibiotic efflux pump;  colistin B;  polymyxin B;  protein(s) and two-component regulatory system modulating antibiotic efflux;  pmr phosphoethanolamine transferase;  colistin A;  macrolide antibiotic;  peptide antibiotic;  efflux pump complex or subunit conferring antibiotic resistance;  antibiotic target alteration;  resistance by absence;  erythromycin; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
UPDATED category_aro_name with resistance by absence
UPDATED category_aro_cvterm_id with 40429
UPDATED category_aro_accession with 3003764
UPDATED category_aro_class_name with Resistance Mechanism
UPDATED category_aro_description with Mechanism of antibiotic resistance conferred by deletion of gene (usually a porin).
UPDATED category_aro_name with polymyxin B
UPDATED category_aro_cvterm_id with 36593
UPDATED category_aro_accession with 3000454
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Polymyxin B is mixture of mostly polymyxins B1 and B2, mainly used for resistant gram-negative infections. They are polypeptides with cationic detergent action on cell membranes.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
"
1603	UPDATE	SHV-86	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  SHV beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1602	UPDATE	AAC(6')-Iai	 antibiotic inactivation;  kanamycin A;  aminoglycoside antibiotic;  AAC(6');  isepamicin;  sisomicin;  arbekacin;  netilmicin;  amikacin;  dibekacin;  neomycin;  tobramycin; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with sisomicin
UPDATED category_aro_cvterm_id with 35953
UPDATED category_aro_accession with 0000035
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.
UPDATED category_aro_name with dibekacin
UPDATED category_aro_cvterm_id with 35926
UPDATED category_aro_accession with 0000007
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.
UPDATED category_aro_name with kanamycin A
UPDATED category_aro_cvterm_id with 35966
UPDATED category_aro_accession with 0000049
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.
UPDATED category_aro_name with arbekacin
UPDATED category_aro_cvterm_id with 36998
UPDATED category_aro_accession with 3000654
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.
UPDATED category_aro_name with netilmicin
UPDATED category_aro_cvterm_id with 35956
UPDATED category_aro_accession with 0000038
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.
UPDATED category_aro_name with amikacin
UPDATED category_aro_cvterm_id with 35932
UPDATED category_aro_accession with 0000013
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.
UPDATED category_aro_name with isepamicin
UPDATED category_aro_cvterm_id with 36996
UPDATED category_aro_accession with 3000652
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.
UPDATED category_aro_name with neomycin
UPDATED category_aro_cvterm_id with 35924
UPDATED category_aro_accession with 0000005
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.
UPDATED category_aro_name with tobramycin
UPDATED category_aro_cvterm_id with 35969
UPDATED category_aro_accession with 0000052
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1605	UPDATE	cphA5	 carbapenem;  CphA beta-lactamase;  antibiotic inactivation; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1604	UPDATE	CTX-M-84	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1607	UPDATE	Streptococcus pneumoniae PBP1a conferring resistance to amoxicillin	 penam;  cephamycin;  cephalosporin;  Penicillin-binding protein mutations conferring resistance to beta-lactam antibiotics;  antibiotic target alteration;  amoxicillin; 	model_description; model_param	"UPDATED model_description with Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
"
1606	UPDATE	CTX-M-16	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1555	UPDATE	SHV-140	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  SHV beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
809	UPDATE	lnuB	 antibiotic inactivation;  lincosamide nucleotidyltransferase (LNU);  lincomycin;  clindamycin;  lincosamide antibiotic; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with lincomycin
UPDATED category_aro_cvterm_id with 35964
UPDATED category_aro_accession with 0000046
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Lincomycin is a lincosamide antibiotic that comes from the actinomyces Streptomyces lincolnensis. It binds to the 23s portion of the 50S subunit of bacterial ribosomes and inhibit early elongation of peptide chain by inhibiting transpeptidase reaction.
UPDATED category_aro_name with clindamycin
UPDATED category_aro_cvterm_id with 35983
UPDATED category_aro_accession with 0000066
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Clindamycin is a lincosamide antibiotic that blocks A-site aminoacyl-tRNA binding. It is usually used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
808	UPDATE	TEM-171	 penam;  antibiotic inactivation;  penem;  cephalosporin;  monobactam;  ampicillin;  TEM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
803	UPDATE	cphA4	 carbapenem;  CphA beta-lactamase;  antibiotic inactivation; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
802	UPDATE	QnrA3	 sparfloxacin;  norfloxacin;  quinolone resistance protein (qnr);  gatifloxacin;  levofloxacin;  antibiotic target protection;  ciprofloxacin;  fluoroquinolone antibiotic;  nalidixic acid;  moxifloxacin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
801	UPDATE	mfpA	 sparfloxacin;  norfloxacin;  quinolone resistance protein (qnr);  gatifloxacin;  levofloxacin;  antibiotic target protection;  ciprofloxacin;  fluoroquinolone antibiotic;  nalidixic acid;  moxifloxacin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
800	UPDATE	CTX-M-87	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
807	UPDATE	OKP-B-1	 penam;  antibiotic inactivation;  OKP beta-lactamase;  cephalosporin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
806	UPDATE	SHV-150	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  SHV beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
805	UPDATE	MexC	 penam;  antibiotic efflux;  resistance-nodulation-cell division (RND) antibiotic efflux pump;  ofloxacin;  trimethoprim;  aminocoumarin antibiotic;  novobiocin;  macrolide antibiotic;  phenicol antibiotic;  efflux pump complex or subunit conferring antibiotic resistance;  cephalosporin;  diaminopyrimidine antibiotic;  tetracycline antibiotic;  gentamicin C;  chloramphenicol;  aminoglycoside antibiotic;  fluoroquinolone antibiotic;  tetracycline;  erythromycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
804	UPDATE	tetB(P)	 chlortetracycline;  demeclocycline;  oxytetracycline;  tetracycline antibiotic;  tetracycline;  antibiotic target protection;  minocycline;  tetracycline-resistant ribosomal protection protein;  doxycycline; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4437	UPDATE	CARB-53	 penam;  antibiotic inactivation;  CARB beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2848	UPDATE	MCR-4.1	 peptide antibiotic;  MCR phosphoethanolamine transferase;  antibiotic target alteration;  colistin B;  colistin A; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2849	UPDATE	MCR-5.1	 peptide antibiotic;  MCR phosphoethanolamine transferase;  antibiotic target alteration;  colistin B;  colistin A; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2846	UPDATE	BUT-1	 BUT beta-lactamase;  antibiotic inactivation;  cephalosporin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2844	UPDATE	Rhodobacter sphaeroides ampC beta-lactamase	 penam;  antibiotic inactivation;  benzylpenicillin;  ampC-type beta-lactamase;  cephalosporin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2845	UPDATE	Laribacter hongkongensis ampC beta-lactamase	 penam;  antibiotic inactivation;  cephalosporin;  ampC-type beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2842	UPDATE	Vibrio cholerae varG	 carbapenem;  antibiotic inactivation;  Subclass B1 Vibrio cholerae varG beta-lactamase;  meropenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2843	UPDATE	Escherichia coli ampC beta-lactamase	 penam;  penicillin;  cephalosporin;  antibiotic inactivation;  ampC-type beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2840	UPDATE	NPS-1	 penam;  antibiotic inactivation;  NPS beta-lactamase;  cephalosporin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2841	UPDATE	Escherichia coli 23S rRNA with mutation conferring resistance to chloramphenicol	 antibiotic target alteration;  phenicol antibiotic;  23S rRNA with mutation conferring resistance to phenicol antibiotics;  chloramphenicol; 	model_description; model_param	"UPDATED model_description with Ribosomal RNA (rRNA) Gene Variant Models (RVM) are similar to Protein Variant Models (PVM), i.e. detect  sequences based on their similarity to a curated reference sequence and secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles, except RVMs are designed to detect AMR acquired via mutation of genes encoding ribosomal RNAs (rRNA). RVMs include a rRNA reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTN bit-score above the curated BLASTN cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTN bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
UPDATED param_description with The BLASTN bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
"
3320	UPDATE	QnrS10	 sparfloxacin;  norfloxacin;  quinolone resistance protein (qnr);  gatifloxacin;  levofloxacin;  antibiotic target protection;  ciprofloxacin;  fluoroquinolone antibiotic;  nalidixic acid;  moxifloxacin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3321	UPDATE	AAC(3)-IIe	 antibiotic inactivation;  AAC(3);  aminoglycoside antibiotic;  gentamicin A; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with gentamicin A
UPDATED category_aro_cvterm_id with 40942
UPDATED category_aro_accession with 3004015
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Gentamicin A is part of a complex of broad spectrum aminoglycoside antibiotics. Gentamicin inhibits protein synthesis, resulting in bacterial cell death.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5474	UPDATE	PDC-344	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3323	UPDATE	QnrS11	 sparfloxacin;  norfloxacin;  quinolone resistance protein (qnr);  gatifloxacin;  levofloxacin;  antibiotic target protection;  ciprofloxacin;  fluoroquinolone antibiotic;  nalidixic acid;  moxifloxacin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3324	UPDATE	Erm(49)	 Erm 23S ribosomal RNA methyltransferase;  erythromycin;  macrolide antibiotic;  antibiotic target alteration;  streptogramin antibiotic;  clindamycin;  lincosamide antibiotic; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with clindamycin
UPDATED category_aro_cvterm_id with 35983
UPDATED category_aro_accession with 0000066
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Clindamycin is a lincosamide antibiotic that blocks A-site aminoacyl-tRNA binding. It is usually used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria.
UPDATED category_aro_name with erythromycin
UPDATED category_aro_cvterm_id with 35925
UPDATED category_aro_accession with 0000006
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure/function processes critical for life or replication are inhibited.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3325	UPDATE	QnrS12	 sparfloxacin;  norfloxacin;  quinolone resistance protein (qnr);  gatifloxacin;  levofloxacin;  antibiotic target protection;  ciprofloxacin;  fluoroquinolone antibiotic;  nalidixic acid;  moxifloxacin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3326	UPDATE	QnrS15	 sparfloxacin;  norfloxacin;  quinolone resistance protein (qnr);  gatifloxacin;  levofloxacin;  antibiotic target protection;  ciprofloxacin;  fluoroquinolone antibiotic;  nalidixic acid;  moxifloxacin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5471	UPDATE	PDC-341	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3328	UPDATE	AAC(6')-Im	 antibiotic inactivation;  AAC(6');  aminoglycoside antibiotic;  kanamycin A;  netilmicin;  amikacin;  dibekacin;  tobramycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3329	UPDATE	Mycoplasma genitalium parC mutations confers resistance to Moxifloxacin	 antibiotic target alteration;  fluoroquinolone resistant parC;  fluoroquinolone antibiotic;  moxifloxacin; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
UPDATED category_aro_name with moxifloxacin
UPDATED category_aro_cvterm_id with 35991
UPDATED category_aro_accession with 0000074
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
"
5478	UPDATE	PDC-349	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5479	UPDATE	PDC-35	 antibiotic inactivation;  avibactam;  ceftolozane;  ceftazidime-avibactam;  cephalosporin;  carbapenem;  ceftazidime;  PDC beta-lactamase;  monobactam;  tazobactam;  ceftolozane-tazobactam; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_description with Serine beta-lactamase inhibitor targeting class A, class C, and some class D enzymes.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1775	UPDATE	QnrS7	 sparfloxacin;  norfloxacin;  quinolone resistance protein (qnr);  gatifloxacin;  levofloxacin;  antibiotic target protection;  ciprofloxacin;  fluoroquinolone antibiotic;  nalidixic acid;  moxifloxacin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1774	UPDATE	CTX-M-106	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1777	UPDATE	OXA-177	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1776	UPDATE	SHV-159	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  SHV beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1771	UPDATE	TEM-19	 penam;  antibiotic inactivation;  penem;  cephalosporin;  monobactam;  ampicillin;  TEM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1770	UPDATE	TEM-127	 penam;  antibiotic inactivation;  penem;  cephalosporin;  monobactam;  ampicillin;  TEM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1773	UPDATE	tet(43)	 tetracycline antibiotic;  efflux pump complex or subunit conferring antibiotic resistance;  major facilitator superfamily (MFS) antibiotic efflux pump;  tetracycline;  antibiotic efflux; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1772	UPDATE	aadA11	 antibiotic inactivation;  aminoglycoside antibiotic;  ANT(3'');  streptomycin;  spectinomycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1779	UPDATE	CTX-M-12	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1778	UPDATE	OKP-A-5	 penam;  antibiotic inactivation;  OKP beta-lactamase;  cephalosporin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
993	UPDATE	AAC(6')-Ib9	 AAC(6');  antibiotic inactivation;  aminoglycoside antibiotic; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
321	UPDATE	CTX-M-35	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
31	UPDATE	CTX-M-155	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
327	UPDATE	GES-17	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  GES beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3502	UPDATE	OXA-429	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1159	UPDATE	TEM-129	 penam;  antibiotic inactivation;  penem;  cephalosporin;  monobactam;  ampicillin;  TEM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1158	UPDATE	SHV-22	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  SHV beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2130	UPDATE	opcM	 efflux pump complex or subunit conferring antibiotic resistance;  fluoroquinolone antibiotic;  aminoglycoside antibiotic;  resistance-nodulation-cell division (RND) antibiotic efflux pump;  antibiotic efflux; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1155	UPDATE	ACT-9	 antibiotic inactivation;  carbapenem;  penam;  ACT beta-lactamase;  cephalosporin;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1154	UPDATE	TEM-146	 penam;  antibiotic inactivation;  penem;  cephalosporin;  monobactam;  ampicillin;  TEM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1157	UPDATE	vanG	 glycopeptide antibiotic;  glycopeptide resistance gene cluster;  Van ligase;  vancomycin;  antibiotic target alteration; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with vancomycin
UPDATED category_aro_cvterm_id with 35947
UPDATED category_aro_accession with 0000028
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.
UPDATED param_value with 250
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1156	UPDATE	Erm(31)	 methymycin;  narbomycin;  Erm 23S ribosomal RNA methyltransferase;  pikromycin;  macrolide antibiotic;  antibiotic target alteration;  streptogramin antibiotic;  lincosamide antibiotic; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
DELETED 35952
UPDATED category_aro_name with methymycin
UPDATED category_aro_cvterm_id with 37631
UPDATED category_aro_accession with 3001232
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Produced by Streptomyces venezuelae ATCC 15439.
UPDATED category_aro_name with narbomycin
UPDATED category_aro_cvterm_id with 37625
UPDATED category_aro_accession with 3001226
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Produced by Streptomyces narbonensis.
UPDATED category_aro_name with pikromycin
UPDATED category_aro_cvterm_id with 37632
UPDATED category_aro_accession with 3001233
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Produced by Streptomyces venezuelae ATCC 15439.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1151	UPDATE	OXA-240	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1150	UPDATE	QnrVC5	 sparfloxacin;  norfloxacin;  quinolone resistance protein (qnr);  gatifloxacin;  levofloxacin;  antibiotic target protection;  ciprofloxacin;  fluoroquinolone antibiotic;  nalidixic acid;  moxifloxacin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1153	UPDATE	KPC-3	 antibiotic inactivation;  penam;  carbapenem;  cephalosporin;  monobactam;  KPC beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1152	UPDATE	CTX-M-39	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5519	UPDATE	PDC-39	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5518	UPDATE	PDC-389	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1488	UPDATE	TEM-75	 penam;  antibiotic inactivation;  penem;  cephalosporin;  monobactam;  ampicillin;  TEM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
30	UPDATE	OXA-226	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5511	UPDATE	PDC-381	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5510	UPDATE	PDC-38	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5513	UPDATE	PDC-383	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5512	UPDATE	PDC-382	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5515	UPDATE	PDC-386	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5514	UPDATE	PDC-385	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5517	UPDATE	PDC-388	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5516	UPDATE	PDC-387	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1551	UPDATE	OXA-78	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1550	UPDATE	smeR	 penam;  antibiotic efflux;  resistance-nodulation-cell division (RND) antibiotic efflux pump;  protein(s) and two-component regulatory system modulating antibiotic efflux;  efflux pump complex or subunit conferring antibiotic resistance;  cephalosporin;  cephamycin;  aminoglycoside antibiotic; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1553	UPDATE	tet(S)	 chlortetracycline;  demeclocycline;  oxytetracycline;  tetracycline antibiotic;  tetracycline;  antibiotic target protection;  minocycline;  tetracycline-resistant ribosomal protection protein;  doxycycline; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1552	UPDATE	MUS-1	 carbapenem;  antibiotic inactivation;  MUS beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
59	UPDATE	OXA-256	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
58	UPDATE	QnrB47	 sparfloxacin;  norfloxacin;  quinolone resistance protein (qnr);  gatifloxacin;  levofloxacin;  antibiotic target protection;  ciprofloxacin;  fluoroquinolone antibiotic;  nalidixic acid;  moxifloxacin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1557	UPDATE	SHV-187	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  SHV beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1556	UPDATE	VIM-13	 penam;  antibiotic inactivation;  penem;  carbapenem;  cephalosporin;  cephamycin;  VIM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
55	UPDATE	OXA-69	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
54	UPDATE	TEM-34	 penam;  antibiotic inactivation;  penem;  cephalosporin;  monobactam;  ampicillin;  TEM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
57	UPDATE	SHV-24	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  SHV beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
56	UPDATE	TEM-7	 penam;  antibiotic inactivation;  penem;  cephalosporin;  monobactam;  ampicillin;  TEM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
51	UPDATE	AAC(3)-IIIc	 antibiotic inactivation;  AAC(3);  aminoglycoside antibiotic;  gentamicin A; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with gentamicin A
UPDATED category_aro_cvterm_id with 40942
UPDATED category_aro_accession with 3004015
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Gentamicin A is part of a complex of broad spectrum aminoglycoside antibiotics. Gentamicin inhibits protein synthesis, resulting in bacterial cell death.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
50	UPDATE	SME-2	 carbapenem;  antibiotic inactivation;  SME beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
53	UPDATE	MOX-5	 penam;  antibiotic inactivation;  MOX beta-lactamase;  cephamycin;  cephalosporin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
52	UPDATE	OXY-2-2	 penam;  OXY beta-lactamase;  cephalosporin;  antibiotic inactivation;  monobactam; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
537	UPDATE	OXA-120	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
536	UPDATE	TEM-95	 penam;  antibiotic inactivation;  penem;  cephalosporin;  monobactam;  ampicillin;  TEM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
535	UPDATE	Morganella morganii gyrB conferring resistance to fluoroquinolones	 fluoroquinolone resistant gyrB;  grepafloxacin;  trovafloxacin;  ofloxacin;  norfloxacin;  nalidixic acid;  lomefloxacin;  gatifloxacin;  levofloxacin;  sparfloxacin;  antibiotic target alteration;  enoxacin;  ciprofloxacin;  pefloxacin;  fluoroquinolone antibiotic;  moxifloxacin; 	model_description; model_param	"UPDATED model_description with Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
"
534	UPDATE	vanV gene in vanB cluster	 glycopeptide antibiotic;  glycopeptide resistance gene cluster;  antibiotic target alteration;  vancomycin;  vanV; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with vancomycin
UPDATED category_aro_cvterm_id with 35947
UPDATED category_aro_accession with 0000028
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
533	UPDATE	CARB-16	 penam;  antibiotic inactivation;  CARB beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
532	UPDATE	CTX-M-47	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
531	UPDATE	SAT-3	 streptothricin acetyltransferase (SAT);  streptothricin;  antibiotic inactivation;  nucleoside antibiotic; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
530	UPDATE	VIM-11	 penam;  antibiotic inactivation;  penem;  carbapenem;  cephalosporin;  cephamycin;  VIM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1518	UPDATE	EreA2	 antibiotic inactivation;  macrolide antibiotic;  macrolide esterase;  erythromycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
539	UPDATE	QnrB59	 sparfloxacin;  norfloxacin;  quinolone resistance protein (qnr);  gatifloxacin;  levofloxacin;  antibiotic target protection;  ciprofloxacin;  fluoroquinolone antibiotic;  nalidixic acid;  moxifloxacin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3571	UPDATE	CIA-2	 carbapenem;  antibiotic inactivation;  cephalosporin;  CIA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1908	UPDATE	OKP-A-6	 penam;  antibiotic inactivation;  OKP beta-lactamase;  cephalosporin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1558	UPDATE	Bacillus subtilis mprF	 peptide antibiotic;  antibiotic target alteration;  defensin resistant mprF;  defensin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1909	UPDATE	AAC(6')-Iak	 AAC(6');  antibiotic inactivation;  aminoglycoside antibiotic; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5605	UPDATE	PDC-64	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5604	UPDATE	PDC-60	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5607	UPDATE	PDC-94	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5606	UPDATE	PDC-71	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5601	UPDATE	PDC-475	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5600	UPDATE	PDC-474	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5603	UPDATE	PDC-58	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5602	UPDATE	PDC-476	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5609	UPDATE	PDC-96	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3296	UPDATE	erm(45)	 pristinamycin IA;  Erm 23S ribosomal RNA methyltransferase;  erythromycin;  macrolide antibiotic;  streptogramin B antibiotic;  antibiotic target alteration;  streptogramin antibiotic;  clindamycin;  lincosamide antibiotic; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with streptogramin B antibiotic
UPDATED category_aro_cvterm_id with 35967
UPDATED category_aro_accession with 0000050
UPDATED category_aro_class_name with Drug Class
UPDATED category_aro_description with Streptogramin B antibiotics are are cyclic hepta- or hexa-depsipeptides.  Type B streptogramins block the peptide exit tunnel of the 50S bacterial ribosome. The general composition of group B streptogramins is 3-hydroxypicolinic acid-L-Thr-D-aminobutyric acid (or D-Ala)-L-Pro-L-Phe (or 4-N-,N-(dimethylamino)-L-Phe)-X-L-phenylglycine. Used alone, streptogramin B antibiotics are bacteriostatic, but is bactericidal when used with streptogramin A antibiotics.
UPDATED category_aro_name with pristinamycin IA
UPDATED category_aro_cvterm_id with 36722
UPDATED category_aro_accession with 3000583
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Pristinamycin IA is a type B streptogramin antibiotic produced by Streptomyces pristinaespiralis. It binds to the P site of the 50S subunit of the bacterial ribosome, preventing the extension of protein chains.
UPDATED category_aro_name with clindamycin
UPDATED category_aro_cvterm_id with 35983
UPDATED category_aro_accession with 0000066
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Clindamycin is a lincosamide antibiotic that blocks A-site aminoacyl-tRNA binding. It is usually used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria.
UPDATED category_aro_name with erythromycin
UPDATED category_aro_cvterm_id with 35925
UPDATED category_aro_accession with 0000006
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure/function processes critical for life or replication are inhibited.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4690	UPDATE	IMP-63	 penam;  antibiotic inactivation;  penem;  carbapenem;  cephalosporin;  IMP beta-lactamase;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1905	UPDATE	ACT-21	 antibiotic inactivation;  carbapenem;  penam;  ACT beta-lactamase;  cephalosporin;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
304	UPDATE	IND-11	 carbapenem;  antibiotic inactivation;  IND beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1419	UPDATE	OXA-454	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1902	UPDATE	OXA-246	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3455	UPDATE	OXA-292	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3291	UPDATE	Erm(48)	 pristinamycin IA;  Erm 23S ribosomal RNA methyltransferase;  erythromycin;  macrolide antibiotic;  streptogramin B antibiotic;  antibiotic target alteration;  streptogramin antibiotic;  clindamycin;  lincosamide antibiotic; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with streptogramin B antibiotic
UPDATED category_aro_cvterm_id with 35967
UPDATED category_aro_accession with 0000050
UPDATED category_aro_class_name with Drug Class
UPDATED category_aro_description with Streptogramin B antibiotics are are cyclic hepta- or hexa-depsipeptides.  Type B streptogramins block the peptide exit tunnel of the 50S bacterial ribosome. The general composition of group B streptogramins is 3-hydroxypicolinic acid-L-Thr-D-aminobutyric acid (or D-Ala)-L-Pro-L-Phe (or 4-N-,N-(dimethylamino)-L-Phe)-X-L-phenylglycine. Used alone, streptogramin B antibiotics are bacteriostatic, but is bactericidal when used with streptogramin A antibiotics.
UPDATED category_aro_name with pristinamycin IA
UPDATED category_aro_cvterm_id with 36722
UPDATED category_aro_accession with 3000583
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Pristinamycin IA is a type B streptogramin antibiotic produced by Streptomyces pristinaespiralis. It binds to the P site of the 50S subunit of the bacterial ribosome, preventing the extension of protein chains.
UPDATED category_aro_name with clindamycin
UPDATED category_aro_cvterm_id with 35983
UPDATED category_aro_accession with 0000066
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Clindamycin is a lincosamide antibiotic that blocks A-site aminoacyl-tRNA binding. It is usually used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria.
UPDATED category_aro_name with erythromycin
UPDATED category_aro_cvterm_id with 35925
UPDATED category_aro_accession with 0000006
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure/function processes critical for life or replication are inhibited.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
429	UPDATE	mdsA	 penam;  antibiotic efflux;  resistance-nodulation-cell division (RND) antibiotic efflux pump;  penem;  carbapenem;  efflux pump complex or subunit conferring antibiotic resistance;  cephalosporin;  cephamycin;  monobactam;  phenicol antibiotic;  chloramphenicol; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
428	UPDATE	OXY-2-7	 penam;  OXY beta-lactamase;  cephalosporin;  antibiotic inactivation;  monobactam; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1900	UPDATE	ACT-13	 antibiotic inactivation;  carbapenem;  penam;  ACT beta-lactamase;  cephalosporin;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1399	UPDATE	OXA-315	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1398	UPDATE	OXA-108	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
421	UPDATE	TEM-2	 penam;  antibiotic inactivation;  penem;  cephalosporin;  monobactam;  ampicillin;  TEM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
420	UPDATE	CTX-M-1	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1395	UPDATE	Neisseria gonorrhoeae porin PIB (por)	 penam;  reduced permeability to antibiotic;  penem;  cephamycin;  carbapenem;  cephalosporin;  penicillin;  General Bacterial Porin with reduced permeability to beta-lactams;  tetracycline antibiotic;  monobactam;  tetracycline; 	model_description; model_param	"UPDATED model_description with Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
UPDATED param_description with A set of nucleotide or amino acid substitutions that are all required to confer resistance to an antibiotic drug or drug class, encoded as: [wild-type 1][position 1][mutation 1],[wild-type 2][position 2][mutation 2], etc. For example, D63Y,T142K.
"
422	UPDATE	FOX-10	 antibiotic inactivation;  cephamycin;  cephalosporin;  FOX beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
425	UPDATE	TEM-182	 penam;  antibiotic inactivation;  penem;  cephalosporin;  monobactam;  ampicillin;  TEM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
424	UPDATE	SHV-36	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  SHV beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1391	UPDATE	CTX-M-92	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1390	UPDATE	arlR	 antibiotic efflux;  major facilitator superfamily (MFS) antibiotic efflux pump;  protein(s) and two-component regulatory system modulating antibiotic efflux;  norfloxacin;  efflux pump complex or subunit conferring antibiotic resistance;  acriflavine;  ciprofloxacin;  fluoroquinolone antibiotic;  disinfecting agents and antiseptics; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3812	UPDATE	ROB-6	 penam;  antibiotic inactivation;  cephalosporin;  ROB beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3813	UPDATE	ROB-7	 penam;  antibiotic inactivation;  cephalosporin;  ROB beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3810	UPDATE	ROB-4	 penam;  antibiotic inactivation;  cephalosporin;  ROB beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3811	UPDATE	ROB-5	 penam;  antibiotic inactivation;  cephalosporin;  ROB beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3816	UPDATE	ROB-10	 penam;  antibiotic inactivation;  cephalosporin;  ROB beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3817	UPDATE	Thermus thermophilus uL3 mutations conferring resistance to pleuromutilin antibiotics	 Ribosomal protein mutation conferring resistance to pleuromutilin antibiotics;  antibiotic target alteration;  pleuromutilin antibiotic;  tiamulin; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
UPDATED category_aro_name with tiamulin
UPDATED category_aro_cvterm_id with 37015
UPDATED category_aro_accession with 3000671
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Tiamulin is a pleuromutilin derivative currently used in veterinary medicine. It binds to the 23 rRNA of the 50S ribosomal subunit to inhibit protein translation.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
"
3814	UPDATE	ROB-2	 penam;  antibiotic inactivation;  cephalosporin;  ROB beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3815	UPDATE	ROB-8	 penam;  antibiotic inactivation;  cephalosporin;  ROB beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3818	UPDATE	Thermus thermophilus 23s rRNA conferring resistance to pleuromutilin antibiotics	 23S rRNA with mutation conferring resistance to pleuromutilin antibiotics;  antibiotic target alteration;  pleuromutilin antibiotic;  tiamulin; 	model_description; ARO_category; model_param	"UPDATED model_description with Ribosomal RNA (rRNA) Gene Variant Models (RVM) are similar to Protein Variant Models (PVM), i.e. detect  sequences based on their similarity to a curated reference sequence and secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles, except RVMs are designed to detect AMR acquired via mutation of genes encoding ribosomal RNAs (rRNA). RVMs include a rRNA reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTN bit-score above the curated BLASTN cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTN bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
UPDATED category_aro_name with tiamulin
UPDATED category_aro_cvterm_id with 37015
UPDATED category_aro_accession with 3000671
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Tiamulin is a pleuromutilin derivative currently used in veterinary medicine. It binds to the 23 rRNA of the 50S ribosomal subunit to inhibit protein translation.
UPDATED param_description with The BLASTN bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
"
3819	UPDATE	dfrA31	 trimethoprim;  diaminopyrimidine antibiotic;  trimethoprim resistant dihydrofolate reductase dfr;  antibiotic target replacement; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
856	UPDATE	mepR	 antibiotic efflux;  protein(s) and two-component regulatory system modulating antibiotic efflux;  multidrug and toxic compound extrusion (MATE) transporter;  efflux pump complex or subunit conferring antibiotic resistance;  tigecycline;  glycylcycline;  tetracycline antibiotic; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
850	UPDATE	OXA-26	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
302	UPDATE	TEM-207	 penam;  antibiotic inactivation;  penem;  cephalosporin;  monobactam;  ampicillin;  TEM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
851	UPDATE	Mycobacterium tuberculosis pncA mutations conferring resistance to pyrazinamide	 antibiotic target alteration;  Pyrazinamide resistant pncA;  pyrazinamide;  pyrazine antibiotic; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Pyrazinamide is an antimycobacterial. It is highly specific and active only against Mycobacterium tuberculosis. This compound is a prodrug and needs to be activated inside the cell. It interferes with the bacterium's ability to synthesize new fatty acids, causing cell death.
UPDATED category_aro_name with pyrazine antibiotic
UPDATED category_aro_cvterm_id with 45737
UPDATED category_aro_accession with 3007155
UPDATED category_aro_class_name with Drug Class
UPDATED category_aro_description with A group of antibiotics derived from pyrazine.
UPDATED param_description with A nucleotide substitution resulting in a change from an amino acid codon to a STOP codon, encoded as [wild type amino acid][position][STOP], for example Q42STOP.
UPDATED param_description with A subtype of the insertion mutation detection model parameter used when a set of insertion mutations are reported in a nucleotide sequence format, encoded as [+]nt[position]:[nucleotides], for example +nt391:GG. Such mutations may be of variable length, possibly causing a frameshift but not causing premature termination or a functional knockout.
UPDATED param_description with A subtype of the deletion mutation detection model parameter used when a set of deletion mutations are reported in a nucleotide sequence format, encoded as [-]nt[position]:[nucleotides], for example -nt25:T.
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
UPDATED param_description with A set of nucleotide or amino acid substitutions that are all required to confer resistance to an antibiotic drug or drug class, encoded as: [wild-type 1][position 1][mutation 1],[wild-type 2][position 2][mutation 2], etc. For example, D63Y,T142K.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4299	UPDATE	ADC-234	 antibiotic inactivation;  cephalosporin;  ADC beta-lactamases pending classification for carbapenemase activity; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4298	UPDATE	ADC-233	 antibiotic inactivation;  cephalosporin;  ADC beta-lactamases pending classification for carbapenemase activity; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4295	UPDATE	ADC-230	 antibiotic inactivation;  cephalosporin;  ADC beta-lactamases pending classification for carbapenemase activity; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4294	UPDATE	ADC-229	 antibiotic inactivation;  cephalosporin;  ADC beta-lactamases pending classification for carbapenemase activity; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4297	UPDATE	ADC-232	 antibiotic inactivation;  cephalosporin;  ADC beta-lactamases pending classification for carbapenemase activity; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4296	UPDATE	ADC-231	 antibiotic inactivation;  cephalosporin;  ADC beta-lactamases pending classification for carbapenemase activity; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4291	UPDATE	ADC-226	 antibiotic inactivation;  cephalosporin;  ADC beta-lactamases pending classification for carbapenemase activity; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4290	UPDATE	ADC-225	 antibiotic inactivation;  cephalosporin;  ADC beta-lactamases pending classification for carbapenemase activity; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4293	UPDATE	ADC-228	 antibiotic inactivation;  cephalosporin;  ADC beta-lactamases pending classification for carbapenemase activity; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4292	UPDATE	ADC-227	 antibiotic inactivation;  cephalosporin;  ADC beta-lactamases pending classification for carbapenemase activity; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
307	UPDATE	CTX-M-101	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1422	UPDATE	ACC-3	 penam;  monobactam;  cephalosporin;  ACC beta-lactamase;  antibiotic inactivation; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5748	UPDATE	mefJ	 efflux pump complex or subunit conferring antibiotic resistance;  major facilitator superfamily (MFS) antibiotic efflux pump;  macrolide antibiotic;  antibiotic efflux; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1426	UPDATE	IMP-7	 penam;  antibiotic inactivation;  penem;  carbapenem;  cephalosporin;  IMP beta-lactamase;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3570	UPDATE	CIA-1	 carbapenem;  antibiotic inactivation;  cephalosporin;  CIA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4749	UPDATE	LHK-4	 carbapenem;  antibiotic inactivation;  cephalosporin;  LHK beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4748	UPDATE	LHK-3	 carbapenem;  antibiotic inactivation;  cephalosporin;  LHK beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1425	UPDATE	RbpA	 rifampin;  rifapentine;  RbpA bacterial RNA polymerase-binding protein;  antibiotic target protection;  rifabutin;  rifaximin;  rifamycin antibiotic; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4743	UPDATE	LEN-27	 penam;  LEN beta-lactamase;  antibiotic inactivation;  penem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4741	UPDATE	KPC-82	 antibiotic inactivation;  penam;  carbapenem;  cephalosporin;  monobactam;  KPC beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4740	UPDATE	KPC-81	 antibiotic inactivation;  penam;  carbapenem;  cephalosporin;  monobactam;  KPC beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4747	UPDATE	LHK-2	 carbapenem;  antibiotic inactivation;  cephalosporin;  LHK beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4746	UPDATE	LHK-1	 carbapenem;  antibiotic inactivation;  cephalosporin;  LHK beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4745	UPDATE	LEN-31	 penam;  LEN beta-lactamase;  antibiotic inactivation;  penem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4744	UPDATE	LEN-28	 penam;  LEN beta-lactamase;  antibiotic inactivation;  penem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1424	UPDATE	OXY-2-4	 penam;  OXY beta-lactamase;  cephalosporin;  antibiotic inactivation;  monobactam; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2331	UPDATE	kdpE	 kanamycin A;  kdpDE;  aminoglycoside antibiotic;  protein(s) and two-component regulatory system modulating antibiotic efflux;  antibiotic efflux; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3475	UPDATE	OXA-341	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
722	UPDATE	vanR gene in vanA cluster	 vanR;  glycopeptide resistance gene cluster;  teicoplanin;  glycopeptide antibiotic;  antibiotic target alteration;  vancomycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2183	UPDATE	glycopeptide resistance gene cluster VanB	 glycopeptide antibiotic;  glycopeptide resistance gene cluster;  antibiotic target alteration;  vancomycin; 	model_description; ARO_category; model_param	"UPDATED model_description with Gene Cluster Meta-Models (PKM) are used to curate spatial clusters of individual genes within operons, such as for glycopeptide resistance gene clusters. The individual genes will have their own individual detection models (e.g. PHM, PVM, POM, etc.) while the PKM checks to see if all the component genes of the cluster have a Strict or Perfect hit and are ordered correctly within an operon. PKMs are encoded using the gene order parameter. This model type is still under development and not currently supported by the Resistance Gene Identifier (RGI) software.
UPDATED category_aro_name with vancomycin
UPDATED category_aro_cvterm_id with 35947
UPDATED category_aro_accession with 0000028
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.
UPDATED param_description with Spatial clusters of genes are encoded using the gene order parameter: [gene type]:[cvterm_id],[gene type]:[cvterm_id], etc. The gene type designations are: R = regulatory, C = core, A = accessory.
"
2182	UPDATE	glycopeptide resistance gene cluster VanD	 glycopeptide antibiotic;  glycopeptide resistance gene cluster;  antibiotic target alteration;  vancomycin;  teicoplanin; 	model_description; ARO_category; model_param	"UPDATED model_description with Gene Cluster Meta-Models (PKM) are used to curate spatial clusters of individual genes within operons, such as for glycopeptide resistance gene clusters. The individual genes will have their own individual detection models (e.g. PHM, PVM, POM, etc.) while the PKM checks to see if all the component genes of the cluster have a Strict or Perfect hit and are ordered correctly within an operon. PKMs are encoded using the gene order parameter. This model type is still under development and not currently supported by the Resistance Gene Identifier (RGI) software.
UPDATED category_aro_name with vancomycin
UPDATED category_aro_cvterm_id with 35947
UPDATED category_aro_accession with 0000028
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.
UPDATED category_aro_name with teicoplanin
UPDATED category_aro_cvterm_id with 35948
UPDATED category_aro_accession with 0000029
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Teicoplanin is a glycopeptide antibiotic used in the prophylaxis and treatment of serious infections caused by Gram-positive bacteria. Teicoplanin has a unique acyl-aliphatic chain, and binds to cell wall precursors to inhibit transglycosylation  and transpeptidation.
UPDATED param_description with Spatial clusters of genes are encoded using the gene order parameter: [gene type]:[cvterm_id],[gene type]:[cvterm_id], etc. The gene type designations are: R = regulatory, C = core, A = accessory.
"
2181	UPDATE	glycopeptide resistance gene cluster VanF	 glycopeptide antibiotic;  glycopeptide resistance gene cluster;  antibiotic target alteration;  vancomycin; 	model_description; ARO_category; model_param	"UPDATED model_description with Gene Cluster Meta-Models (PKM) are used to curate spatial clusters of individual genes within operons, such as for glycopeptide resistance gene clusters. The individual genes will have their own individual detection models (e.g. PHM, PVM, POM, etc.) while the PKM checks to see if all the component genes of the cluster have a Strict or Perfect hit and are ordered correctly within an operon. PKMs are encoded using the gene order parameter. This model type is still under development and not currently supported by the Resistance Gene Identifier (RGI) software.
UPDATED category_aro_name with vancomycin
UPDATED category_aro_cvterm_id with 35947
UPDATED category_aro_accession with 0000028
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.
UPDATED param_description with Spatial clusters of genes are encoded using the gene order parameter: [gene type]:[cvterm_id],[gene type]:[cvterm_id], etc. The gene type designations are: R = regulatory, C = core, A = accessory.
"
2180	UPDATE	glycopeptide resistance gene cluster VanL	 glycopeptide antibiotic;  glycopeptide resistance gene cluster;  antibiotic target alteration;  vancomycin; 	model_description; ARO_category; model_param	"UPDATED model_description with Gene Cluster Meta-Models (PKM) are used to curate spatial clusters of individual genes within operons, such as for glycopeptide resistance gene clusters. The individual genes will have their own individual detection models (e.g. PHM, PVM, POM, etc.) while the PKM checks to see if all the component genes of the cluster have a Strict or Perfect hit and are ordered correctly within an operon. PKMs are encoded using the gene order parameter. This model type is still under development and not currently supported by the Resistance Gene Identifier (RGI) software.
UPDATED category_aro_name with vancomycin
UPDATED category_aro_cvterm_id with 35947
UPDATED category_aro_accession with 0000028
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.
UPDATED param_description with Spatial clusters of genes are encoded using the gene order parameter: [gene type]:[cvterm_id],[gene type]:[cvterm_id], etc. The gene type designations are: R = regulatory, C = core, A = accessory.
"
2186	UPDATE	glycopeptide resistance gene cluster VanG	 glycopeptide antibiotic;  glycopeptide resistance gene cluster;  antibiotic target alteration;  vancomycin; 	model_description; ARO_category; model_param	"UPDATED model_description with Gene Cluster Meta-Models (PKM) are used to curate spatial clusters of individual genes within operons, such as for glycopeptide resistance gene clusters. The individual genes will have their own individual detection models (e.g. PHM, PVM, POM, etc.) while the PKM checks to see if all the component genes of the cluster have a Strict or Perfect hit and are ordered correctly within an operon. PKMs are encoded using the gene order parameter. This model type is still under development and not currently supported by the Resistance Gene Identifier (RGI) software.
UPDATED category_aro_name with vancomycin
UPDATED category_aro_cvterm_id with 35947
UPDATED category_aro_accession with 0000028
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.
UPDATED param_description with Spatial clusters of genes are encoded using the gene order parameter: [gene type]:[cvterm_id],[gene type]:[cvterm_id], etc. The gene type designations are: R = regulatory, C = core, A = accessory.
"
2185	UPDATE	glycopeptide resistance gene cluster VanM	 glycopeptide antibiotic;  glycopeptide resistance gene cluster;  antibiotic target alteration;  vancomycin;  teicoplanin; 	model_description; ARO_category; model_param	"UPDATED model_description with Gene Cluster Meta-Models (PKM) are used to curate spatial clusters of individual genes within operons, such as for glycopeptide resistance gene clusters. The individual genes will have their own individual detection models (e.g. PHM, PVM, POM, etc.) while the PKM checks to see if all the component genes of the cluster have a Strict or Perfect hit and are ordered correctly within an operon. PKMs are encoded using the gene order parameter. This model type is still under development and not currently supported by the Resistance Gene Identifier (RGI) software.
UPDATED category_aro_name with vancomycin
UPDATED category_aro_cvterm_id with 35947
UPDATED category_aro_accession with 0000028
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.
UPDATED category_aro_name with teicoplanin
UPDATED category_aro_cvterm_id with 35948
UPDATED category_aro_accession with 0000029
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Teicoplanin is a glycopeptide antibiotic used in the prophylaxis and treatment of serious infections caused by Gram-positive bacteria. Teicoplanin has a unique acyl-aliphatic chain, and binds to cell wall precursors to inhibit transglycosylation  and transpeptidation.
UPDATED param_description with Spatial clusters of genes are encoded using the gene order parameter: [gene type]:[cvterm_id],[gene type]:[cvterm_id], etc. The gene type designations are: R = regulatory, C = core, A = accessory.
"
228	UPDATE	sdiA	 penam;  antibiotic efflux;  triclosan;  rifampin;  resistance-nodulation-cell division (RND) antibiotic efflux pump;  protein(s) and two-component regulatory system modulating antibiotic efflux;  efflux pump complex or subunit conferring antibiotic resistance;  disinfecting agents and antiseptics;  tetracycline antibiotic;  cephalosporin;  cefalotin;  tigecycline;  glycylcycline;  ampicillin;  fluoroquinolone antibiotic;  rifamycin antibiotic;  phenicol antibiotic;  tetracycline;  chloramphenicol; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
227	UPDATE	OKP-B-3	 penam;  antibiotic inactivation;  OKP beta-lactamase;  cephalosporin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
226	UPDATE	OXA-113	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
225	UPDATE	CTX-M-88	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
224	UPDATE	MIR-2	 antibiotic inactivation;  monobactam;  cephalosporin;  MIR beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
223	UPDATE	GES-3	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  GES beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
222	UPDATE	JOHN-1	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  JOHN beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
221	UPDATE	CMY-100	 antibiotic inactivation;  CMY beta-lactamase;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
220	UPDATE	TEM-92	 penam;  antibiotic inactivation;  penem;  cephalosporin;  monobactam;  ampicillin;  TEM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2213	UPDATE	opmE	 kitasamycin;  imipenem;  thiamphenicol;  resistance-nodulation-cell division (RND) antibiotic efflux pump;  rokitamycin;  antibiotic efflux;  trimethoprim;  macrolide antibiotic;  disinfecting agents and antiseptics;  carbapenem;  efflux pump complex or subunit conferring antibiotic resistance;  diaminopyrimidine antibiotic;  acriflavine;  tetracycline antibiotic;  chloramphenicol;  phenicol antibiotic;  tetracycline;  erythromycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2212	UPDATE	mexQ	 kitasamycin;  imipenem;  thiamphenicol;  resistance-nodulation-cell division (RND) antibiotic efflux pump;  rokitamycin;  antibiotic efflux;  trimethoprim;  macrolide antibiotic;  disinfecting agents and antiseptics;  carbapenem;  efflux pump complex or subunit conferring antibiotic resistance;  diaminopyrimidine antibiotic;  acriflavine;  tetracycline antibiotic;  chloramphenicol;  phenicol antibiotic;  tetracycline;  erythromycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2211	UPDATE	mexP	 kitasamycin;  imipenem;  thiamphenicol;  resistance-nodulation-cell division (RND) antibiotic efflux pump;  rokitamycin;  antibiotic efflux;  trimethoprim;  macrolide antibiotic;  disinfecting agents and antiseptics;  carbapenem;  efflux pump complex or subunit conferring antibiotic resistance;  diaminopyrimidine antibiotic;  acriflavine;  tetracycline antibiotic;  chloramphenicol;  phenicol antibiotic;  tetracycline;  erythromycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1427	UPDATE	acrD	 efflux pump complex or subunit conferring antibiotic resistance;  aminoglycoside antibiotic;  resistance-nodulation-cell division (RND) antibiotic efflux pump;  antibiotic efflux; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2217	UPDATE	mexN	 antibiotic efflux;  thiamphenicol;  resistance-nodulation-cell division (RND) antibiotic efflux pump;  efflux pump complex or subunit conferring antibiotic resistance;  phenicol antibiotic;  chloramphenicol; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2216	UPDATE	mexM	 antibiotic efflux;  thiamphenicol;  resistance-nodulation-cell division (RND) antibiotic efflux pump;  efflux pump complex or subunit conferring antibiotic resistance;  phenicol antibiotic;  chloramphenicol; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2215	UPDATE	Pseudomonas aeruginosa gyrA and parC conferring resistance to fluoroquinolones	 ofloxacin;  fluoroquinolone resistant parC;  pefloxacin;  ciprofloxacin;  antibiotic target alteration;  fluoroquinolone antibiotic; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
UPDATED category_aro_name with ofloxacin
UPDATED category_aro_cvterm_id with 37007
UPDATED category_aro_accession with 3000663
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Ofloxacin is a 6-fluoro, 7-piperazinyl quinolone with a methyl-substituted oxazine ring. It has a broad spectrum of activity including many enterobacteria and mycoplasma but most anaerobes are resistant.
UPDATED category_aro_name with pefloxacin
UPDATED category_aro_cvterm_id with 37142
UPDATED category_aro_accession with 3000762
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Pefloxacin is structurally and functionally similar to norfloxacin. It is poorly active against mycobacteria, while anaerobes are resistant.
UPDATED category_aro_name with ciprofloxacin
UPDATED category_aro_cvterm_id with 35954
UPDATED category_aro_accession with 0000036
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
"
2799	UPDATE	AxyY	 antibiotic efflux;  resistance-nodulation-cell division (RND) antibiotic efflux pump;  macrolide antibiotic;  efflux pump complex or subunit conferring antibiotic resistance;  cephalosporin;  cefepime;  fluoroquinolone antibiotic;  aminoglycoside antibiotic;  erythromycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2219	UPDATE	MexL	 antibiotic efflux;  triclosan;  resistance-nodulation-cell division (RND) antibiotic efflux pump;  protein(s) and two-component regulatory system modulating antibiotic efflux;  macrolide antibiotic;  efflux pump complex or subunit conferring antibiotic resistance;  tetracycline antibiotic;  disinfecting agents and antiseptics;  tetracycline;  erythromycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2337	UPDATE	ADC-4	 antibiotic inactivation;  cephalosporin;  ADC beta-lactamase without carbapenemase activity; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1089	UPDATE	CMY-14	 antibiotic inactivation;  CMY beta-lactamase;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5475	UPDATE	PDC-345	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2786	UPDATE	Burkholderia pseudomallei Omp38	 penam;  reduced permeability to antibiotic;  imipenem;  penem;  benzylpenicillin;  cephalosporin;  carbapenem;  ceftazidime;  cephamycin;  General Bacterial Porin with reduced permeability to beta-lactams;  monobactam;  cefoxitin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1167	UPDATE	norB	 antibiotic efflux;  major facilitator superfamily (MFS) antibiotic efflux pump;  sparfloxacin;  norfloxacin;  efflux pump complex or subunit conferring antibiotic resistance;  ciprofloxacin;  fluoroquinolone antibiotic;  moxifloxacin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
151	UPDATE	OKP-A-15	 penam;  antibiotic inactivation;  OKP beta-lactamase;  cephalosporin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
150	UPDATE	catB3	 antibiotic inactivation;  thiamphenicol;  chloramphenicol acetyltransferase (CAT);  azidamfenicol;  phenicol antibiotic;  chloramphenicol; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
153	UPDATE	adeF	 antibiotic efflux;  resistance-nodulation-cell division (RND) antibiotic efflux pump;  efflux pump complex or subunit conferring antibiotic resistance;  tetracycline antibiotic;  fluoroquinolone antibiotic;  tetracycline; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
152	UPDATE	cpxA	 antibiotic efflux;  resistance-nodulation-cell division (RND) antibiotic efflux pump;  protein(s) and two-component regulatory system modulating antibiotic efflux;  aminocoumarin antibiotic;  novobiocin;  efflux pump complex or subunit conferring antibiotic resistance;  aminoglycoside antibiotic; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
155	UPDATE	TEM-195	 penam;  antibiotic inactivation;  penem;  cephalosporin;  monobactam;  ampicillin;  TEM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
154	UPDATE	mgrA	 penam;  peptide antibiotic;  ATP-binding cassette (ABC) antibiotic efflux pump;  major facilitator superfamily (MFS) antibiotic efflux pump;  protein(s) and two-component regulatory system modulating antibiotic efflux;  antibiotic efflux;  sparfloxacin;  norfloxacin;  disinfecting agents and antiseptics;  moxifloxacin;  daptomycin;  cefotaxime;  efflux pump complex or subunit conferring antibiotic resistance;  cephalosporin;  acriflavine;  ciprofloxacin;  tetracycline antibiotic;  moenomycin A1;  fluoroquinolone antibiotic;  methicillin;  tetracycline; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
157	UPDATE	dfrA21	 trimethoprim;  diaminopyrimidine antibiotic;  trimethoprim resistant dihydrofolate reductase dfr;  antibiotic target replacement; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
156	UPDATE	AAC(6')-Iaf	 antibiotic inactivation;  AAC(6');  aminoglycoside antibiotic;  kanamycin A;  amikacin;  dibekacin; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with kanamycin A
UPDATED category_aro_cvterm_id with 35966
UPDATED category_aro_accession with 0000049
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.
UPDATED category_aro_name with amikacin
UPDATED category_aro_cvterm_id with 35932
UPDATED category_aro_accession with 0000013
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.
UPDATED category_aro_name with dibekacin
UPDATED category_aro_cvterm_id with 35926
UPDATED category_aro_accession with 0000007
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
159	UPDATE	vgaALC	 virginiamycin M1;  pleuromutilin antibiotic;  vga-type ABC-F protein;  streptogramin A antibiotic;  lincomycin;  antibiotic target protection;  streptogramin antibiotic;  clindamycin;  lincosamide antibiotic; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with lincomycin
UPDATED category_aro_cvterm_id with 35964
UPDATED category_aro_accession with 0000046
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Lincomycin is a lincosamide antibiotic that comes from the actinomyces Streptomyces lincolnensis. It binds to the 23s portion of the 50S subunit of bacterial ribosomes and inhibit early elongation of peptide chain by inhibiting transpeptidase reaction.
UPDATED category_aro_name with virginiamycin M1
UPDATED category_aro_cvterm_id with 37013
UPDATED category_aro_accession with 3000669
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Virginiamycin M1 is a streptogramin A antibiotic.
UPDATED category_aro_name with clindamycin
UPDATED category_aro_cvterm_id with 35983
UPDATED category_aro_accession with 0000066
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Clindamycin is a lincosamide antibiotic that blocks A-site aminoacyl-tRNA binding. It is usually used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria.
UPDATED category_aro_name with lincosamide antibiotic
UPDATED category_aro_cvterm_id with 35936
UPDATED category_aro_accession with 0000017
UPDATED category_aro_class_name with Drug Class
UPDATED category_aro_description with Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
158	UPDATE	myrA	 mycinamicin;  macrolide antibiotic;  non-erm 23S ribosomal RNA methyltransferase (G748);  antibiotic target alteration;  tylosin;  lincosamide antibiotic; 	ARO_description; model_description; ARO_category; model_param	"UPDATED ARO_description with myrA is a methyltransferase found in Micromonospora griseorubida and confers resistance to mycinamicin and tylosin. Specifically, this enzyme adds a methyl group to guanosine 748 (E. coli numbering) of 23S ribosomal RNA. MyrA is found in the mycinamicin biosynthetic cluster and is one mechanism by which M. griseorubida protects itself from self-destruction when producing this macrolide.
UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with mycinamicin
UPDATED category_aro_cvterm_id with 37623
UPDATED category_aro_accession with 3001224
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Produced by Micromonospora griseorubida.
UPDATED category_aro_name with tylosin
UPDATED category_aro_cvterm_id with 36284
UPDATED category_aro_accession with 3000145
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Tylosin is a 16-membered macrolide, naturally produced by Streptomyces fradiae. It interacts with the bacterial ribosome 50S subunit to inhibit protein synthesis.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1293	UPDATE	OXA-197	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2430	UPDATE	hp1181	 metronidazole;  major facilitator superfamily (MFS) antibiotic efflux pump;  efflux pump complex or subunit conferring antibiotic resistance;  antibiotic efflux;  nitroimidazole antibiotic;  ciprofloxacin;  tetracycline antibiotic;  fluoroquinolone antibiotic;  tetracycline; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1088	UPDATE	Staphylococcus aureus rpoB mutants conferring resistance to daptomycin	 peptide antibiotic;  daptomycin resistant beta-subunit of RNA polymerase (rpoB);  antibiotic target alteration;  daptomycin;  rifamycin antibiotic; 	model_description; model_param	"UPDATED model_description with Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
"
2436	UPDATE	D-Ala-D-Ala ligase	 glycopeptide antibiotic;  antibiotic target alteration;  Van ligase;  vancomycin; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
UPDATED category_aro_name with vancomycin
UPDATED category_aro_cvterm_id with 35947
UPDATED category_aro_accession with 0000028
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.
UPDATED param_description with A subtype of the insertion mutation detection model parameter used when a set of insertion mutations are reported in a nucleotide sequence format, encoded as [+]nt[position]:[nucleotides], for example +nt391:GG. Such mutations may be of variable length, possibly causing a frameshift but not causing premature termination or a functional knockout.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
UPDATED param_description with A subtype of the deletion mutation detection model parameter used when a set of deletion mutations are reported in a peptide sequence format, encoded as [-][AAs][position range], for example -K527 or -QN517-518.
"
2435	UPDATE	lmrP	 antibiotic efflux;  major facilitator superfamily (MFS) antibiotic efflux pump;  macrolide antibiotic;  efflux pump complex or subunit conferring antibiotic resistance;  tetracycline antibiotic;  streptogramin antibiotic;  lincosamide antibiotic; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2434	UPDATE	Klebsiella pneumoniae OmpK36	 penam;  reduced permeability to antibiotic;  penem;  carbapenem;  cephalosporin;  cefalotin;  cephamycin;  General Bacterial Porin with reduced permeability to beta-lactams;  monobactam;  resistance by absence;  ceftriaxone; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Knockout Models (PKM) reflect resistance by the absence of a gene product, most often deletion of a gene involved in antibiotic import, such as Vibrio cholerae OmpT. Like Protein Homolog Models (PHMs), PKMs include a reference sequence and a bitscore cut-off for detection using BLASTP but instead are designed to only report lack of detection under Perfect or Strict criteria. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff. This model type is still under development and not currently supported by the Resistance Gene Identifier (RGI) software.
UPDATED category_aro_name with cefalotin
UPDATED category_aro_cvterm_id with 37084
UPDATED category_aro_accession with 3000704
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Cefalotin is a semisynthetic cephalosporin antibiotic activate against staphylococci. It is resistant to staphylococci beta-lactamases but hydrolyzed by enterobacterial beta-lactamases.
UPDATED category_aro_name with ceftriaxone
UPDATED category_aro_cvterm_id with 35979
UPDATED category_aro_accession with 0000062
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Ceftriaxone is a third-generation cephalosporin antibiotic. The presence of an aminothiazolyl sidechain increases ceftriazone's resistance to beta-lactamases. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4202	UPDATE	ADC-131	 antibiotic inactivation;  cephalosporin;  ADC beta-lactamases pending classification for carbapenemase activity; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4203	UPDATE	ADC-132	 antibiotic inactivation;  cephalosporin;  ADC beta-lactamases pending classification for carbapenemase activity; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1161	UPDATE	lsaB	 pleuromutilin;  pleuromutilin antibiotic;  lsa-type ABC-F protein;  antibiotic target protection;  streptogramin antibiotic;  clindamycin;  lincosamide antibiotic; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4518	UPDATE	CTX-M-189	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4519	UPDATE	CTX-M-190	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4512	UPDATE	CTX-M-183	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4513	UPDATE	CTX-M-184	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4510	UPDATE	CTX-M-181	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4511	UPDATE	CTX-M-182	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4516	UPDATE	CTX-M-187	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4517	UPDATE	CTX-M-188	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4514	UPDATE	CTX-M-185	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4515	UPDATE	CTX-M-186	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1359	UPDATE	OXA-233	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1162	UPDATE	aadA15	 antibiotic inactivation;  aminoglycoside antibiotic;  ANT(3'');  streptomycin;  spectinomycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4205	UPDATE	ADC-134	 antibiotic inactivation;  cephalosporin;  ADC beta-lactamases pending classification for carbapenemase activity; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1428	UPDATE	cphA2	 carbapenem;  CphA beta-lactamase;  antibiotic inactivation; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5289	UPDATE	PDC-151	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5288	UPDATE	PDC-150	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2724	UPDATE	MuxABC-OpmB	 kitasamycin;  resistance-nodulation-cell division (RND) antibiotic efflux pump;  rokitamycin;  aztreonam;  aminocoumarin antibiotic;  novobiocin;  macrolide antibiotic;  antibiotic efflux;  efflux pump complex or subunit conferring antibiotic resistance;  tetracycline antibiotic;  monobactam;  tetracycline;  erythromycin; 	model_description; model_param	"UPDATED model_description with Efflux Pump System Meta-Models (EPS) are dedicated to efflux complexes and their regulators, such as AcrAB-TolC. Using the efflux pump components parameter, this model type simply includes a list of detection models for each component of the complex. This model type is still under development and not currently supported by the Resistance Gene Identifier (RGI) software.
UPDATED param_description with Association of proteins within efflux protein complexes or regulatory networks are encoded by the efflux pump components parameter: model_id,model_id,model_id, etc.
"
2720	UPDATE	MuxC	 kitasamycin;  resistance-nodulation-cell division (RND) antibiotic efflux pump;  rokitamycin;  aztreonam;  aminocoumarin antibiotic;  novobiocin;  macrolide antibiotic;  antibiotic efflux;  efflux pump complex or subunit conferring antibiotic resistance;  tetracycline antibiotic;  monobactam;  tetracycline;  erythromycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5281	UPDATE	PDC-144	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5280	UPDATE	PDC-143	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5283	UPDATE	PDC-146	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5282	UPDATE	PDC-145	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5285	UPDATE	PDC-148	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5284	UPDATE	PDC-147	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2729	UPDATE	MexJK-OprM	 antibiotic efflux;  resistance-nodulation-cell division (RND) antibiotic efflux pump;  macrolide antibiotic;  efflux pump complex or subunit conferring antibiotic resistance;  tetracycline antibiotic;  tetracycline;  erythromycin; 	model_description; model_param	"UPDATED model_description with Efflux Pump System Meta-Models (EPS) are dedicated to efflux complexes and their regulators, such as AcrAB-TolC. Using the efflux pump components parameter, this model type simply includes a list of detection models for each component of the complex. This model type is still under development and not currently supported by the Resistance Gene Identifier (RGI) software.
UPDATED param_description with Association of proteins within efflux protein complexes or regulatory networks are encoded by the efflux pump components parameter: model_id,model_id,model_id, etc.
"
5286	UPDATE	PDC-149	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
280	UPDATE	CTX-M-11	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1163	UPDATE	CMY-94	 antibiotic inactivation;  CMY beta-lactamase;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5049	UPDATE	OXA-740	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5048	UPDATE	OXA-739	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5047	UPDATE	OXA-738	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5046	UPDATE	OXA-736	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5045	UPDATE	OXA-735	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5044	UPDATE	OXA-734	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5043	UPDATE	OXA-733	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5042	UPDATE	OXA-732	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5041	UPDATE	OXA-731	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5040	UPDATE	OXA-730	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1807	UPDATE	OXA-70	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1806	UPDATE	OXA-14	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1805	UPDATE	TEM-131	 penam;  antibiotic inactivation;  penem;  cephalosporin;  monobactam;  ampicillin;  TEM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1804	UPDATE	OXA-107	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1803	UPDATE	QnrVC3	 sparfloxacin;  norfloxacin;  quinolone resistance protein (qnr);  gatifloxacin;  levofloxacin;  antibiotic target protection;  ciprofloxacin;  fluoroquinolone antibiotic;  nalidixic acid;  moxifloxacin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1802	UPDATE	OXA-168	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1801	UPDATE	AAC(6')-Ib11	 antibiotic inactivation;  AAC(6');  kanamycin A;  amikacin;  aminoglycoside antibiotic;  gentamicin A;  tobramycin; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with kanamycin A
UPDATED category_aro_cvterm_id with 35966
UPDATED category_aro_accession with 0000049
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.
UPDATED category_aro_name with amikacin
UPDATED category_aro_cvterm_id with 35932
UPDATED category_aro_accession with 0000013
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.
UPDATED category_aro_name with gentamicin A
UPDATED category_aro_cvterm_id with 40942
UPDATED category_aro_accession with 3004015
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Gentamicin A is part of a complex of broad spectrum aminoglycoside antibiotics. Gentamicin inhibits protein synthesis, resulting in bacterial cell death.
UPDATED category_aro_name with tobramycin
UPDATED category_aro_cvterm_id with 35969
UPDATED category_aro_accession with 0000052
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1800	UPDATE	SHV-120	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  SHV beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3788	UPDATE	SatA	 streptothricin acetyltransferase (SAT);  streptothricin;  antibiotic inactivation;  nucleoside antibiotic; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with streptothricin
UPDATED category_aro_cvterm_id with 35931
UPDATED category_aro_accession with 0000012
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Streptothricins are a group of N-glycoside antibiotics that include a carbamoylated D-glucosamine to which are attached a series of L-beta-lysine residues at position 2 and a streptolidine at position 1.  Streptothricins vary by the number of beta-lysine residues (from 1 (nourseothricin) to 7) and target protein synthesis in bacteria and eukaryotes.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3789	UPDATE	BLMT	 glycopeptide antibiotic;  antibiotic inactivation;  Bleomycin resistant protein;  bleomycin; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with bleomycin
UPDATED category_aro_cvterm_id with 35970
UPDATED category_aro_accession with 0000053
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Bleomycin is a family of glycopeptide antibiotics produced by the bacterium Streptomyces verticillus. Bleomycins, taken as a mixture, act by the induction of DNA and RNA strand breaks. In addition to its antibacterial activity, bleomycin is also used as an anticancer agent.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1809	UPDATE	QnrB5	 sparfloxacin;  norfloxacin;  quinolone resistance protein (qnr);  gatifloxacin;  levofloxacin;  antibiotic target protection;  ciprofloxacin;  fluoroquinolone antibiotic;  nalidixic acid;  moxifloxacin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1808	UPDATE	tet(A)	 tetracycline antibiotic;  efflux pump complex or subunit conferring antibiotic resistance;  major facilitator superfamily (MFS) antibiotic efflux pump;  tetracycline;  antibiotic efflux; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4996	UPDATE	OXA-684	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4997	UPDATE	OXA-685	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4994	UPDATE	OXA-682	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4995	UPDATE	OXA-683	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4992	UPDATE	OXA-679	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4993	UPDATE	OXA-680	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4990	UPDATE	OXA-677	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4991	UPDATE	OXA-678	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
126	UPDATE	TEM-183	 penam;  antibiotic inactivation;  penem;  cephalosporin;  monobactam;  ampicillin;  TEM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4998	UPDATE	OXA-686	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4999	UPDATE	OXA-687	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1547	UPDATE	vanR gene in vanC cluster	 glycopeptide antibiotic;  glycopeptide resistance gene cluster;  antibiotic target alteration;  vanR;  vancomycin; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with vancomycin
UPDATED category_aro_cvterm_id with 35947
UPDATED category_aro_accession with 0000028
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1403	UPDATE	OXA-388	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1183	UPDATE	tet(Q)	 chlortetracycline;  demeclocycline;  oxytetracycline;  tetracycline antibiotic;  tetracycline;  antibiotic target protection;  minocycline;  tetracycline-resistant ribosomal protection protein;  doxycycline; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5265	UPDATE	PDC-129	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3258	UPDATE	dfrA27	 trimethoprim;  diaminopyrimidine antibiotic;  trimethoprim resistant dihydrofolate reductase dfr;  antibiotic target replacement; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3259	UPDATE	dfrA28	 trimethoprim;  diaminopyrimidine antibiotic;  trimethoprim resistant dihydrofolate reductase dfr;  antibiotic target replacement; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1948	UPDATE	TEM-167	 penam;  antibiotic inactivation;  penem;  cephalosporin;  monobactam;  ampicillin;  TEM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1949	UPDATE	cphA6	 carbapenem;  CphA beta-lactamase;  antibiotic inactivation; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1257	UPDATE	QnrB68	 sparfloxacin;  norfloxacin;  quinolone resistance protein (qnr);  gatifloxacin;  levofloxacin;  antibiotic target protection;  ciprofloxacin;  fluoroquinolone antibiotic;  nalidixic acid;  moxifloxacin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1942	UPDATE	BJP-1	 carbapenem;  antibiotic inactivation;  BJP beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1943	UPDATE	Mycobacterium tuberculosis kasA mutant conferring resistance to isoniazid	 isoniazid;  antibiotic target alteration;  antibiotic resistant kasA;  isoniazid-like antibiotic; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_name with isoniazid-like antibiotic
UPDATED category_aro_cvterm_id with 45734
UPDATED category_aro_accession with 3007152
UPDATED category_aro_class_name with Drug Class
UPDATED category_aro_description with A group of antibiotics containing isoniazid and its derivatives.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
"
1940	UPDATE	QnrB30	 sparfloxacin;  norfloxacin;  quinolone resistance protein (qnr);  gatifloxacin;  levofloxacin;  antibiotic target protection;  ciprofloxacin;  fluoroquinolone antibiotic;  nalidixic acid;  moxifloxacin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1941	UPDATE	SHV-98	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  SHV beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1946	UPDATE	CTX-M-10	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1947	UPDATE	CTX-M-160	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3256	UPDATE	dfrA9	 trimethoprim;  diaminopyrimidine antibiotic;  trimethoprim resistant dihydrofolate reductase dfr;  antibiotic target replacement; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1945	UPDATE	SHV-50	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  SHV beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
818	UPDATE	SHV-141	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  SHV beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
819	UPDATE	CTX-M-68	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1255	UPDATE	OXA-119	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
810	UPDATE	mecC	 penam;  methicillin resistant PBP2;  methicillin;  antibiotic target replacement; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with methicillin
UPDATED category_aro_cvterm_id with 35934
UPDATED category_aro_accession with 0000015
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Derived from penicillin to combat penicillin-resistance, methicillin is insensitive to beta-lactamases (also known as penicillinases) secreted by many penicillin-resistant bacteria. Methicillin is bactericidal, and acts by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
811	UPDATE	TEM-26	 penam;  antibiotic inactivation;  penem;  cephalosporin;  monobactam;  ampicillin;  TEM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
812	UPDATE	CMY-10	 antibiotic inactivation;  CMY beta-lactamase;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
813	UPDATE	OXA-216	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
814	UPDATE	TEM-113	 penam;  antibiotic inactivation;  penem;  cephalosporin;  monobactam;  ampicillin;  TEM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
815	UPDATE	GOB-1	 carbapenem;  penam;  GOB beta-lactamase;  antibiotic inactivation;  cephalosporin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
816	UPDATE	OXA-3	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
817	UPDATE	CTX-M-158	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2859	UPDATE	PDC-80	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1991	UPDATE	otr(C)	 tetracycline antibiotic;  efflux pump complex or subunit conferring antibiotic resistance;  ATP-binding cassette (ABC) antibiotic efflux pump;  tetracycline;  antibiotic efflux; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1250	UPDATE	CTX-M-96	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5183	UPDATE	OXA-886	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2851	UPDATE	Escherichia coli gyrA with mutation conferring resistance to triclosan	 antibiotic target alteration;  triclosan;  disinfecting agents and antiseptics;  triclosan resistant gyrA; 	model_description; model_param	"UPDATED model_description with Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
"
2850	UPDATE	Salmonella enterica gyrA with mutation conferring resistance to triclosan	 antibiotic target alteration;  triclosan;  disinfecting agents and antiseptics;  triclosan resistant gyrA; 	model_description; model_param	"UPDATED model_description with Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
"
2853	UPDATE	PDC-74	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1251	UPDATE	CTX-M-157	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2855	UPDATE	PDC-76	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1621	UPDATE	SHV-45	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  SHV beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2857	UPDATE	PDC-78	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2856	UPDATE	PDC-77	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5461	UPDATE	PDC-331	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5460	UPDATE	PDC-330	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5463	UPDATE	PDC-333	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5462	UPDATE	PDC-332	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1494	UPDATE	LAT-1	 antibiotic inactivation;  CMY beta-lactamase;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5464	UPDATE	PDC-334	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5467	UPDATE	PDC-338	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5466	UPDATE	PDC-336	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1498	UPDATE	cphA8	 carbapenem;  CphA beta-lactamase;  antibiotic inactivation; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5468	UPDATE	PDC-339	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3339	UPDATE	dfrA15b	 trimethoprim;  diaminopyrimidine antibiotic;  trimethoprim resistant dihydrofolate reductase dfr;  antibiotic target replacement; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3338	UPDATE	AAC(6')-Iag	 antibiotic inactivation;  kanamycin A;  aminoglycoside antibiotic;  AAC(6');  isepamicin;  sisomicin;  arbekacin;  amikacin;  dibekacin;  tobramycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
423	UPDATE	DHA-16	 antibiotic inactivation;  cephalosporin;  cephamycin;  DHA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1626	UPDATE	vgaE	 virginiamycin M1;  pleuromutilin antibiotic;  tiamulin;  vga-type ABC-F protein;  streptogramin A antibiotic;  antibiotic target protection;  streptogramin antibiotic;  clindamycin;  lincosamide antibiotic; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with virginiamycin M1
UPDATED category_aro_cvterm_id with 37013
UPDATED category_aro_accession with 3000669
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Virginiamycin M1 is a streptogramin A antibiotic.
UPDATED category_aro_name with tiamulin
UPDATED category_aro_cvterm_id with 37015
UPDATED category_aro_accession with 3000671
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Tiamulin is a pleuromutilin derivative currently used in veterinary medicine. It binds to the 23 rRNA of the 50S ribosomal subunit to inhibit protein translation.
UPDATED category_aro_name with clindamycin
UPDATED category_aro_cvterm_id with 35983
UPDATED category_aro_accession with 0000066
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Clindamycin is a lincosamide antibiotic that blocks A-site aminoacyl-tRNA binding. It is usually used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria.
UPDATED category_aro_name with lincosamide antibiotic
UPDATED category_aro_cvterm_id with 35936
UPDATED category_aro_accession with 0000017
UPDATED category_aro_class_name with Drug Class
UPDATED category_aro_description with Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1700	UPDATE	ACT-28	 antibiotic inactivation;  carbapenem;  penam;  ACT beta-lactamase;  cephalosporin;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1701	UPDATE	Erm(39)	 streptogramin A antibiotic;  antibiotic target alteration;  virginiamycin S2;  vernamycin C;  pristinamycin IC;  patricin B;  patricin A;  oleandomycin;  ostreogrycin B3;  macrolide antibiotic;  telithromycin;  tylosin;  lincosamide antibiotic;  dirithromycin;  clarithromycin;  clindamycin;  dalfopristin;  pristinamycin IB;  quinupristin;  pristinamycin IA;  Erm 23S ribosomal RNA methyltransferase;  virginiamycin M1;  madumycin II;  griseoviridin;  streptogramin B antibiotic;  lincomycin;  streptogramin antibiotic;  roxithromycin;  spiramycin;  azithromycin;  erythromycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1702	UPDATE	MIR-1	 antibiotic inactivation;  monobactam;  cephalosporin;  MIR beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5264	UPDATE	PDC-128	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1704	UPDATE	CMY-57	 antibiotic inactivation;  CMY beta-lactamase;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1705	UPDATE	SHV-111	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  SHV beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1706	UPDATE	OXA-142	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1707	UPDATE	QnrB4	 sparfloxacin;  norfloxacin;  quinolone resistance protein (qnr);  gatifloxacin;  levofloxacin;  antibiotic target protection;  ciprofloxacin;  fluoroquinolone antibiotic;  nalidixic acid;  moxifloxacin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1708	UPDATE	tet(36)	 chlortetracycline;  demeclocycline;  oxytetracycline;  tetracycline antibiotic;  tetracycline;  antibiotic target protection;  minocycline;  tetracycline-resistant ribosomal protection protein;  doxycycline; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1393	UPDATE	THIN-B	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  THIN-B beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1168	UPDATE	NDM-9	 antibiotic inactivation;  penam;  carbapenem;  cephalosporin;  cephamycin;  NDM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1996	UPDATE	vanX gene in vanM cluster	 antibiotic target alteration;  glycopeptide resistance gene cluster;  teicoplanin;  glycopeptide antibiotic;  vanX;  vancomycin; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with vancomycin
UPDATED category_aro_cvterm_id with 35947
UPDATED category_aro_accession with 0000028
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.
UPDATED category_aro_name with teicoplanin
UPDATED category_aro_cvterm_id with 35948
UPDATED category_aro_accession with 0000029
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Teicoplanin is a glycopeptide antibiotic used in the prophylaxis and treatment of serious infections caused by Gram-positive bacteria. Teicoplanin has a unique acyl-aliphatic chain, and binds to cell wall precursors to inhibit transglycosylation  and transpeptidation.
UPDATED param_value with 200
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2097	UPDATE	Escherichia coli 16S rRNA (rrsB) mutation conferring resistance to paromomycin	 antibiotic target alteration;  aminoglycoside antibiotic;  16s rRNA with mutation conferring resistance to aminoglycoside antibiotics;  paromomycin; 	model_description; model_param	"UPDATED model_description with Ribosomal RNA (rRNA) Gene Variant Models (RVM) are similar to Protein Variant Models (PVM), i.e. detect  sequences based on their similarity to a curated reference sequence and secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles, except RVMs are designed to detect AMR acquired via mutation of genes encoding ribosomal RNAs (rRNA). RVMs include a rRNA reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTN bit-score above the curated BLASTN cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTN bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
UPDATED param_description with The BLASTN bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
"
5269	UPDATE	PDC-132	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1392	UPDATE	aadA22	 antibiotic inactivation;  aminoglycoside antibiotic;  ANT(3'');  streptomycin;  spectinomycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2333	UPDATE	LEN-26	 penam;  LEN beta-lactamase;  antibiotic inactivation;  penem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2096	UPDATE	Escherichia coli 16S rRNA (rrsC) mutation conferring resistance to kasugamicin	 antibiotic target alteration;  aminoglycoside antibiotic;  16s rRNA with mutation conferring resistance to aminoglycoside antibiotics;  kasugamycin; 	model_description; model_param	"UPDATED model_description with Ribosomal RNA (rRNA) Gene Variant Models (RVM) are similar to Protein Variant Models (PVM), i.e. detect  sequences based on their similarity to a curated reference sequence and secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles, except RVMs are designed to detect AMR acquired via mutation of genes encoding ribosomal RNAs (rRNA). RVMs include a rRNA reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTN bit-score above the curated BLASTN cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTN bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
UPDATED param_description with The BLASTN bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
"
427	UPDATE	OCH-7	 penam;  antibiotic inactivation;  penem;  cephalosporin;  cephamycin;  monobactam;  OCH beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2091	UPDATE	Mycobacteroides chelonae 16S rRNA mutation conferring resistance to gentamicin C	 antibiotic target alteration;  gentamicin C;  aminoglycoside antibiotic;  16s rRNA with mutation conferring resistance to aminoglycoside antibiotics; 	model_description; model_param	"UPDATED model_description with Ribosomal RNA (rRNA) Gene Variant Models (RVM) are similar to Protein Variant Models (PVM), i.e. detect  sequences based on their similarity to a curated reference sequence and secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles, except RVMs are designed to detect AMR acquired via mutation of genes encoding ribosomal RNAs (rRNA). RVMs include a rRNA reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTN bit-score above the curated BLASTN cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTN bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
UPDATED param_description with The BLASTN bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
"
426	UPDATE	aadK	 antibiotic inactivation;  streptomycin;  aminoglycoside antibiotic;  ANT(6); 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5188	UPDATE	OXA-891	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2090	UPDATE	Mycobacteroides abscessus 16S rRNA mutation conferring resistance to kanamycin	 kanamycin A;  antibiotic target alteration;  aminoglycoside antibiotic;  16s rRNA with mutation conferring resistance to aminoglycoside antibiotics; 	model_description; model_param	"UPDATED model_description with Ribosomal RNA (rRNA) Gene Variant Models (RVM) are similar to Protein Variant Models (PVM), i.e. detect  sequences based on their similarity to a curated reference sequence and secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles, except RVMs are designed to detect AMR acquired via mutation of genes encoding ribosomal RNAs (rRNA). RVMs include a rRNA reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTN bit-score above the curated BLASTN cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTN bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
UPDATED param_description with The BLASTN bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
"
1128	UPDATE	OXA-23	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1129	UPDATE	CMY-19	 antibiotic inactivation;  CMY beta-lactamase;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5189	UPDATE	OXA-892	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2093	UPDATE	Chlamydophila psittaci 16S rRNA mutation conferring resistance to spectinomycin	 antibiotic target alteration;  aminoglycoside antibiotic;  spectinomycin;  16s rRNA with mutation conferring resistance to aminoglycoside antibiotics; 	model_description; model_param	"UPDATED model_description with Ribosomal RNA (rRNA) Gene Variant Models (RVM) are similar to Protein Variant Models (PVM), i.e. detect  sequences based on their similarity to a curated reference sequence and secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles, except RVMs are designed to detect AMR acquired via mutation of genes encoding ribosomal RNAs (rRNA). RVMs include a rRNA reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTN bit-score above the curated BLASTN cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTN bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
UPDATED param_description with The BLASTN bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
"
1120	UPDATE	IMI-7	 carbapenem;  antibiotic inactivation;  IMI beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1121	UPDATE	APH(3')-VIa	 antibiotic inactivation;  aminoglycoside antibiotic;  isepamicin;  paromomycin;  kanamycin A;  APH(3');  gentamicin B;  amikacin;  ribostamycin;  G418;  neomycin;  butirosin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1122	UPDATE	OXA-180	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1123	UPDATE	FOX-8	 antibiotic inactivation;  cephamycin;  cephalosporin;  FOX beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1124	UPDATE	TEM-186	 penam;  antibiotic inactivation;  penem;  cephalosporin;  monobactam;  ampicillin;  TEM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1125	UPDATE	OKP-B-11	 penam;  antibiotic inactivation;  OKP beta-lactamase;  cephalosporin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1126	UPDATE	OXA-184	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1127	UPDATE	CTX-M-64	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3654	UPDATE	Neisseria gonorrhoeae gyrB conferring resistance to zoliflodacin	 antibiotic target alteration;  Zoliflodacin resistant gyrB;  zoliflodacin-like antibiotic; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
DELETED 42994
UPDATED category_aro_name with zoliflodacin-like antibiotic
UPDATED category_aro_cvterm_id with 45742
UPDATED category_aro_accession with 3007160
UPDATED category_aro_class_name with Drug Class
UPDATED category_aro_description with A group of antibiotics including the experimental compound zoliflodacin and its derivatives.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
"
305	UPDATE	chrB	 mycinamicin;  chalcomycin;  macrolide antibiotic;  non-erm 23S ribosomal RNA methyltransferase (G748);  antibiotic target alteration;  tylosin;  lincosamide antibiotic; 	ARO_description; model_description; ARO_category; model_param	"UPDATED ARO_description with ChrB is a methyltransferase found in Streptomyces bikiniensis and confers resistance to chalcomycin, mycinamicin, and tylosin. Specifically, this enzyme adds a methyl group to guanosine 748 (E. coli numbering). chrB is found in the chalcomycin biosynthetic cluster and is responsible for self-resistance in S. bikiniensis.
UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with mycinamicin
UPDATED category_aro_cvterm_id with 37623
UPDATED category_aro_accession with 3001224
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Produced by Micromonospora griseorubida.
UPDATED category_aro_name with tylosin
UPDATED category_aro_cvterm_id with 36284
UPDATED category_aro_accession with 3000145
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Tylosin is a 16-membered macrolide, naturally produced by Streptomyces fradiae. It interacts with the bacterial ribosome 50S subunit to inhibit protein synthesis.
UPDATED category_aro_name with chalcomycin
UPDATED category_aro_cvterm_id with 37621
UPDATED category_aro_accession with 3001222
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Produced by Streptomyces bikiniensis.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3373	UPDATE	FosD	 antibiotic inactivation;  fosfomycin thiol transferase;  phosphonic acid antibiotic; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
DELETED 35944
UPDATED category_aro_name with phosphonic acid antibiotic
UPDATED category_aro_cvterm_id with 45731
UPDATED category_aro_accession with 3007149
UPDATED category_aro_class_name with Drug Class
UPDATED category_aro_description with A group of antibiotics derived from phosphonic acids.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3024	UPDATE	KPC-24	 antibiotic inactivation;  penam;  carbapenem;  cephalosporin;  monobactam;  KPC beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2098	UPDATE	Mycolicibacterium smegmatis 16S rRNA (rrsB) mutation conferring resistance to viomycin	 peptide antibiotic;  antibiotic target alteration;  16s rRNA with mutation conferring resistance to peptide antibiotics;  viomycin; 	model_description; model_param	"UPDATED model_description with Ribosomal RNA (rRNA) Gene Variant Models (RVM) are similar to Protein Variant Models (PVM), i.e. detect  sequences based on their similarity to a curated reference sequence and secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles, except RVMs are designed to detect AMR acquired via mutation of genes encoding ribosomal RNAs (rRNA). RVMs include a rRNA reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTN bit-score above the curated BLASTN cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTN bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
UPDATED param_description with The BLASTN bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
"
524	UPDATE	dfrA25	 trimethoprim;  diaminopyrimidine antibiotic;  trimethoprim resistant dihydrofolate reductase dfr;  antibiotic target replacement; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
525	UPDATE	CMY-13	 antibiotic inactivation;  CMY beta-lactamase;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
526	UPDATE	ACT-2	 antibiotic inactivation;  carbapenem;  penam;  ACT beta-lactamase;  cephalosporin;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
527	UPDATE	SHV-38	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  SHV beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1018	UPDATE	APH(3')-IIc	 antibiotic inactivation;  aminoglycoside antibiotic;  paromomycin;  kanamycin A;  APH(3');  gentamicin B;  ribostamycin;  G418;  neomycin;  butirosin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1019	UPDATE	IMP-21	 penam;  antibiotic inactivation;  penem;  carbapenem;  cephalosporin;  IMP beta-lactamase;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
522	UPDATE	floR	 antibiotic efflux;  major facilitator superfamily (MFS) antibiotic efflux pump;  efflux pump complex or subunit conferring antibiotic resistance;  florfenicol;  phenicol antibiotic;  chloramphenicol; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
523	UPDATE	OXA-75	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1014	UPDATE	SHV-25	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  SHV beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1015	UPDATE	evgA	 penam;  antibiotic efflux;  major facilitator superfamily (MFS) antibiotic efflux pump;  resistance-nodulation-cell division (RND) antibiotic efflux pump;  protein(s) and two-component regulatory system modulating antibiotic efflux;  norfloxacin;  macrolide antibiotic;  efflux pump complex or subunit conferring antibiotic resistance;  oxacillin;  tetracycline antibiotic;  cloxacillin;  fluoroquinolone antibiotic;  tetracycline;  erythromycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1016	UPDATE	OXA-255	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1017	UPDATE	CTX-M-86	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1010	UPDATE	TEM-209	 penam;  antibiotic inactivation;  penem;  cephalosporin;  monobactam;  ampicillin;  TEM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
529	UPDATE	SHV-185	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  SHV beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1012	UPDATE	KPC-5	 antibiotic inactivation;  penam;  carbapenem;  cephalosporin;  monobactam;  KPC beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1013	UPDATE	APH(2'')-IIIa	 antibiotic inactivation;  kanamycin A;  gentamicin B;  aminoglycoside antibiotic;  sisomicin;  arbekacin;  APH(2'');  netilmicin;  gentamicin C;  amikacin;  isepamicin;  gentamicin A;  tobramycin; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with gentamicin A
UPDATED category_aro_cvterm_id with 40942
UPDATED category_aro_accession with 3004015
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Gentamicin A is part of a complex of broad spectrum aminoglycoside antibiotics. Gentamicin inhibits protein synthesis, resulting in bacterial cell death.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1234	UPDATE	MIR-13	 antibiotic inactivation;  monobactam;  cephalosporin;  MIR beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1235	UPDATE	AAC(6')-Ib'	 AAC(6');  antibiotic inactivation;  amikacin;  aminoglycoside antibiotic;  tobramycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1236	UPDATE	CMY-53	 antibiotic inactivation;  CMY beta-lactamase;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1237	UPDATE	Mycobacterium tuberculosis rpoB mutants conferring resistance to rifampicin	 rifampin;  rifapentine;  rifabutin;  rifamycin-resistant beta-subunit of RNA polymerase (rpoB);  antibiotic target replacement;  antibiotic target alteration;  rifaximin;  rifamycin antibiotic; 	model_description; model_param	"UPDATED model_description with Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
UPDATED param_description with A nucleotide substitution resulting in a change from an amino acid codon to a STOP codon, encoded as [wild type amino acid][position][STOP], for example Q42STOP.
UPDATED param_description with A subtype of the insertion mutation detection model parameter is used when a set of insertion mutations are reported in a peptide sequence format, encoded as [+][AAs][position range], for example +D345 or +MPL110-112.
UPDATED param_description with A subtype of the deletion mutation detection model parameter used when a set of deletion mutations are reported in a peptide sequence format, encoded as [-][AAs][position range], for example -K527 or -QN517-518.
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
UPDATED param_description with A set of nucleotide or amino acid substitutions that are all required to confer resistance to an antibiotic drug or drug class, encoded as: [wild-type 1][position 1][mutation 1],[wild-type 2][position 2][mutation 2], etc. For example, D63Y,T142K.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1230	UPDATE	CTX-M-33	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1231	UPDATE	mel	 macrolide antibiotic;  telithromycin;  msr-type ABC-F protein;  antibiotic target protection;  streptogramin antibiotic;  erythromycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1232	UPDATE	cmeR	 antibiotic efflux;  resistance-nodulation-cell division (RND) antibiotic efflux pump;  protein(s) and two-component regulatory system modulating antibiotic efflux;  macrolide antibiotic;  cefotaxime;  efflux pump complex or subunit conferring antibiotic resistance;  cephalosporin;  fusidane antibiotic;  fusidic acid;  fluoroquinolone antibiotic;  erythromycin; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_name with fusidane antibiotic
UPDATED category_aro_cvterm_id with 45735
UPDATED category_aro_accession with 3007153
UPDATED category_aro_class_name with Drug Class
UPDATED category_aro_description with A group of antibiotics possessing steroid rings or steroid-like structures.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1233	UPDATE	tet(32)	 chlortetracycline;  demeclocycline;  oxytetracycline;  tetracycline antibiotic;  tetracycline;  antibiotic target protection;  minocycline;  tetracycline-resistant ribosomal protection protein;  doxycycline; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4196	UPDATE	ADC-123	 antibiotic inactivation;  cephalosporin;  ADC beta-lactamases pending classification for carbapenemase activity; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4197	UPDATE	ADC-125	 antibiotic inactivation;  cephalosporin;  ADC beta-lactamases pending classification for carbapenemase activity; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4194	UPDATE	ADC-121	 antibiotic inactivation;  cephalosporin;  ADC beta-lactamases pending classification for carbapenemase activity; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4195	UPDATE	ADC-122	 antibiotic inactivation;  cephalosporin;  ADC beta-lactamases pending classification for carbapenemase activity; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1238	UPDATE	OXA-397	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1239	UPDATE	SHV-81	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  SHV beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4190	UPDATE	ADC-116	 antibiotic inactivation;  cephalosporin;  ADC beta-lactamases pending classification for carbapenemase activity; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4191	UPDATE	ADC-117	 antibiotic inactivation;  cephalosporin;  ADC beta-lactamases pending classification for carbapenemase activity; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5670	UPDATE	TER-1	 carbapenem;  TER beta-lactamase;  cephalosporin;  antibiotic inactivation; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5671	UPDATE	TER-2	 carbapenem;  TER beta-lactamase;  cephalosporin;  antibiotic inactivation; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5672	UPDATE	TTU-1	 carbapenem;  antibiotic inactivation;  TTU beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5673	UPDATE	VEB-10	 antibiotic inactivation;  monobactam;  cephalosporin;  VEB beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4358	UPDATE	ALG11-1	 carbapenem;  antibiotic inactivation;  ALG11 beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5675	UPDATE	VEB-12	 antibiotic inactivation;  monobactam;  cephalosporin;  VEB beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5676	UPDATE	VEB-13	 antibiotic inactivation;  monobactam;  cephalosporin;  VEB beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5677	UPDATE	VEB-14	 antibiotic inactivation;  monobactam;  cephalosporin;  VEB beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5678	UPDATE	VEB-15	 antibiotic inactivation;  monobactam;  cephalosporin;  VEB beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4355	UPDATE	ADC-99	 antibiotic inactivation;  cephalosporin;  ADC beta-lactamases pending classification for carbapenemase activity; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4356	UPDATE	AFM-1	 carbapenem;  antibiotic inactivation;  AFM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4357	UPDATE	AFM-2	 carbapenem;  antibiotic inactivation;  AFM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4350	UPDATE	ADC-94	 antibiotic inactivation;  cephalosporin;  ADC beta-lactamases pending classification for carbapenemase activity; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4351	UPDATE	ADC-95	 antibiotic inactivation;  cephalosporin;  ADC beta-lactamases pending classification for carbapenemase activity; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4352	UPDATE	ADC-96	 antibiotic inactivation;  cephalosporin;  ADC beta-lactamases pending classification for carbapenemase activity; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4353	UPDATE	ADC-97	 antibiotic inactivation;  cephalosporin;  ADC beta-lactamases pending classification for carbapenemase activity; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1092	UPDATE	tet(39)	 tetracycline antibiotic;  efflux pump complex or subunit conferring antibiotic resistance;  major facilitator superfamily (MFS) antibiotic efflux pump;  tetracycline;  antibiotic efflux; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1965	UPDATE	LEN-11	 penam;  LEN beta-lactamase;  antibiotic inactivation;  penem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
438	UPDATE	VIM-6	 penam;  antibiotic inactivation;  penem;  carbapenem;  cephalosporin;  cephamycin;  VIM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
439	UPDATE	SHV-83	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  SHV beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
436	UPDATE	OXY-4-1	 penam;  OXY beta-lactamase;  cephalosporin;  antibiotic inactivation;  monobactam; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
437	UPDATE	SHV-69	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  SHV beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
434	UPDATE	LEN-16	 penam;  LEN beta-lactamase;  antibiotic inactivation;  penem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
435	UPDATE	OKP-A-9	 penam;  antibiotic inactivation;  OKP beta-lactamase;  cephalosporin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
433	UPDATE	ACT-25	 antibiotic inactivation;  carbapenem;  penam;  ACT beta-lactamase;  cephalosporin;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
430	UPDATE	OXA-87	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
431	UPDATE	Escherichia coli AcrAB-TolC with MarR mutations conferring resistance to ciprofloxacin and tetracycline	 penam;  antibiotic efflux;  triclosan;  rifampin;  resistance-nodulation-cell division (RND) antibiotic efflux pump;  protein(s) and two-component regulatory system modulating antibiotic efflux;  efflux pump complex or subunit conferring antibiotic resistance;  antibiotic target alteration;  disinfecting agents and antiseptics;  tetracycline antibiotic;  cephalosporin;  cefalotin;  tigecycline;  glycylcycline;  ampicillin;  fluoroquinolone antibiotic;  rifamycin antibiotic;  phenicol antibiotic;  tetracycline;  chloramphenicol; 	model_description; model_param	"UPDATED model_description with Protein Overexpression Models (POM) are similar to Protein Variant Models (PVM) in that they include a protein reference sequence, a curated BLASTP bitscore cut-off, and mapped resistance variants. Whereas PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, reporting only those with curated mutations conferring AMR, POMs are restricted to regulatory proteins and report both wild-type sequences and/or sequences with mutations leading to overexpression of efflux complexes. The former lead to efflux of antibiotics at basal levels, while the latter can confer clinical resistance. POMs include a protein reference sequence (often from wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Perfect RGI match is 100% identical to the wild-type reference protein sequence along its entire length, a Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value may or may not contain at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off may or may not contain at least one curated mutation from amongst the mapped resistance variants.
UPDATED param_description with A nucleotide substitution resulting in a change from an amino acid codon to a STOP codon, encoded as [wild type amino acid][position][STOP], for example Q42STOP.
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4674	UPDATE	IMI-20	 carbapenem;  antibiotic inactivation;  IMI beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3809	UPDATE	ROB-3	 penam;  antibiotic inactivation;  cephalosporin;  ROB beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3808	UPDATE	ROB-13	 penam;  antibiotic inactivation;  cephalosporin;  ROB beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3805	UPDATE	ParS	 erythromycin;  penem;  tetracycline antibiotic;  meropenem;  antibiotic efflux;  imipenem;  resistance-nodulation-cell division (RND) antibiotic efflux pump;  ofloxacin;  norfloxacin;  macrolide antibiotic;  reduced permeability to antibiotic;  carbapenem;  cephalosporin;  ciprofloxacin;  gentamicin C;  amikacin;  aminoglycoside antibiotic;  disinfecting agents and antiseptics;  protein(s) and two-component regulatory system modulating antibiotic efflux;  penam;  Outer Membrane Porin (Opr);  efflux pump complex or subunit conferring antibiotic resistance;  cephamycin;  acriflavine;  monobactam;  fluoroquinolone antibiotic;  chloramphenicol;  phenicol antibiotic;  tetracycline;  tobramycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3804	UPDATE	cprS	 pmr phosphoethanolamine transferase;  peptide antibiotic;  antibiotic target alteration;  protein(s) and two-component regulatory system modulating antibiotic efflux;  antibiotic efflux; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3807	UPDATE	rsmA	 antibiotic efflux;  resistance-nodulation-cell division (RND) antibiotic efflux pump;  protein(s) and two-component regulatory system modulating antibiotic efflux;  trimethoprim;  efflux pump complex or subunit conferring antibiotic resistance;  diaminopyrimidine antibiotic;  fluoroquinolone antibiotic;  phenicol antibiotic;  chloramphenicol; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3806	UPDATE	ParR	 erythromycin;  penem;  tetracycline antibiotic;  meropenem;  antibiotic efflux;  imipenem;  resistance-nodulation-cell division (RND) antibiotic efflux pump;  ofloxacin;  norfloxacin;  macrolide antibiotic;  reduced permeability to antibiotic;  carbapenem;  cephalosporin;  ciprofloxacin;  gentamicin C;  amikacin;  aminoglycoside antibiotic;  disinfecting agents and antiseptics;  protein(s) and two-component regulatory system modulating antibiotic efflux;  penam;  Outer Membrane Porin (Opr);  efflux pump complex or subunit conferring antibiotic resistance;  cephamycin;  acriflavine;  monobactam;  fluoroquinolone antibiotic;  chloramphenicol;  phenicol antibiotic;  tetracycline;  tobramycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3801	UPDATE	AAC(3)-IVb	 antibiotic inactivation;  AAC(3);  aminoglycoside antibiotic;  gentamicin A;  tobramycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3800	UPDATE	OXA-837	 antibiotic inactivation;  penam;  carbapenem;  cephalosporin;  ampicillin;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3803	UPDATE	cprR	 pmr phosphoethanolamine transferase;  peptide antibiotic;  antibiotic target alteration;  protein(s) and two-component regulatory system modulating antibiotic efflux;  antibiotic efflux; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3802	UPDATE	ANT(3'')-Ib	 antibiotic inactivation;  aminoglycoside antibiotic;  ANT(3'');  streptomycin;  spectinomycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1630	UPDATE	IMP-13	 penam;  antibiotic inactivation;  penem;  carbapenem;  cephalosporin;  IMP beta-lactamase;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4671	UPDATE	IMI-17	 carbapenem;  antibiotic inactivation;  IMI beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2864	UPDATE	PDC-85	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4906	UPDATE	OXA-580	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2865	UPDATE	PDC-86	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5708	UPDATE	VIM-59	 penam;  antibiotic inactivation;  penem;  carbapenem;  cephalosporin;  cephamycin;  VIM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5709	UPDATE	VIM-60	 penam;  antibiotic inactivation;  penem;  carbapenem;  cephalosporin;  cephamycin;  VIM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5704	UPDATE	VIM-55	 penam;  antibiotic inactivation;  penem;  carbapenem;  cephalosporin;  cephamycin;  VIM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5705	UPDATE	VIM-56	 penam;  antibiotic inactivation;  penem;  carbapenem;  cephalosporin;  cephamycin;  VIM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5706	UPDATE	VIM-57	 penam;  antibiotic inactivation;  penem;  carbapenem;  cephalosporin;  cephamycin;  VIM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5707	UPDATE	VIM-58	 penam;  antibiotic inactivation;  penem;  carbapenem;  cephalosporin;  cephamycin;  VIM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5700	UPDATE	VIM-51	 penam;  antibiotic inactivation;  penem;  carbapenem;  cephalosporin;  cephamycin;  VIM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5701	UPDATE	VIM-52	 penam;  antibiotic inactivation;  penem;  carbapenem;  cephalosporin;  cephamycin;  VIM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5702	UPDATE	VIM-53	 penam;  antibiotic inactivation;  penem;  carbapenem;  cephalosporin;  cephamycin;  VIM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5703	UPDATE	VIM-54	 penam;  antibiotic inactivation;  penem;  carbapenem;  cephalosporin;  cephamycin;  VIM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2868	UPDATE	PDC-89	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2869	UPDATE	PDC-90	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2249	UPDATE	LpxA	 peptide antibiotic;  antibiotic target alteration;  colistin B;  colistin A;  Acinetobacter mutant Lpx gene conferring resistance to colistin; 	model_description; model_param	"UPDATED model_description with Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A subtype of the deletion mutation detection model parameter used when a set of deletion mutations are reported in a nucleotide sequence format, encoded as [-]nt[position]:[nucleotides], for example -nt25:T.
"
634	UPDATE	smeF	 antibiotic efflux;  resistance-nodulation-cell division (RND) antibiotic efflux pump;  macrolide antibiotic;  efflux pump complex or subunit conferring antibiotic resistance;  tetracycline antibiotic;  fluoroquinolone antibiotic;  phenicol antibiotic;  tetracycline;  chloramphenicol; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1851	UPDATE	KPC-13	 antibiotic inactivation;  penam;  carbapenem;  cephalosporin;  monobactam;  KPC beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1960	UPDATE	smeB	 penam;  antibiotic efflux;  resistance-nodulation-cell division (RND) antibiotic efflux pump;  efflux pump complex or subunit conferring antibiotic resistance;  cephalosporin;  cephamycin;  aminoglycoside antibiotic; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4776	UPDATE	MYO-1	 carbapenem;  antibiotic inactivation;  MYO beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4777	UPDATE	MYX-1	 carbapenem;  antibiotic inactivation;  MYX beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4774	UPDATE	MOX-13	 penam;  antibiotic inactivation;  MOX beta-lactamase;  cephamycin;  cephalosporin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4775	UPDATE	MOX-14	 penam;  antibiotic inactivation;  MOX beta-lactamase;  cephamycin;  cephalosporin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4772	UPDATE	MOX-11	 penam;  antibiotic inactivation;  MOX beta-lactamase;  cephamycin;  cephalosporin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4773	UPDATE	MOX-12	 penam;  antibiotic inactivation;  MOX beta-lactamase;  cephamycin;  cephalosporin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4770	UPDATE	MOR-2	 antibiotic inactivation;  cephalosporin;  MOR beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4771	UPDATE	MOX-10	 penam;  antibiotic inactivation;  MOX beta-lactamase;  cephamycin;  cephalosporin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4778	UPDATE	NDM-26	 antibiotic inactivation;  penam;  carbapenem;  cephalosporin;  cephamycin;  NDM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4779	UPDATE	NDM-30	 antibiotic inactivation;  penam;  carbapenem;  cephalosporin;  cephamycin;  NDM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4174	UPDATE	ACT-84	 antibiotic inactivation;  carbapenem;  penam;  ACT beta-lactamase;  cephalosporin;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4175	UPDATE	ACT-87	 antibiotic inactivation;  carbapenem;  penam;  ACT beta-lactamase;  cephalosporin;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4176	UPDATE	ADC-100	 antibiotic inactivation;  cephalosporin;  ADC beta-lactamases pending classification for carbapenemase activity; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4177	UPDATE	ADC-101	 antibiotic inactivation;  cephalosporin;  ADC beta-lactamases pending classification for carbapenemase activity; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4170	UPDATE	ACT-80	 antibiotic inactivation;  carbapenem;  penam;  ACT beta-lactamase;  cephalosporin;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4171	UPDATE	ACT-81	 antibiotic inactivation;  carbapenem;  penam;  ACT beta-lactamase;  cephalosporin;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4172	UPDATE	ACT-82	 antibiotic inactivation;  carbapenem;  penam;  ACT beta-lactamase;  cephalosporin;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4173	UPDATE	ACT-83	 antibiotic inactivation;  carbapenem;  penam;  ACT beta-lactamase;  cephalosporin;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1961	UPDATE	TEM-105	 penam;  antibiotic inactivation;  penem;  cephalosporin;  monobactam;  ampicillin;  TEM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4178	UPDATE	ADC-102	 antibiotic inactivation;  cephalosporin;  ADC beta-lactamases pending classification for carbapenemase activity; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4179	UPDATE	ADC-103	 antibiotic inactivation;  cephalosporin;  ADC beta-lactamases pending classification for carbapenemase activity; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4904	UPDATE	OXA-578	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4888	UPDATE	OXA-559	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4889	UPDATE	OXA-560	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4918	UPDATE	OXA-592	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4619	UPDATE	GES-36	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  GES beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4618	UPDATE	GES-35	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  GES beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
238	UPDATE	SHV-137	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  SHV beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
239	UPDATE	OXA-83	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
234	UPDATE	QnrS8	 sparfloxacin;  norfloxacin;  quinolone resistance protein (qnr);  gatifloxacin;  levofloxacin;  antibiotic target protection;  ciprofloxacin;  fluoroquinolone antibiotic;  nalidixic acid;  moxifloxacin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
235	UPDATE	OXA-181	 penam;  antibiotic inactivation;  cephalosporin;  carbapenem;  piperacillin-tazobactam;  amoxicillin;  clavulanic acid;  piperacillin;  tazobactam;  OXA beta-lactamase;  amoxicillin-clavulanic acid; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
236	UPDATE	ACT-19	 antibiotic inactivation;  carbapenem;  penam;  ACT beta-lactamase;  cephalosporin;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
237	UPDATE	Chryseobacterium meningosepticum BlaB	 carbapenem;  penam;  antibiotic inactivation;  BlaB beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
230	UPDATE	OXA-422	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
231	UPDATE	OXA-178	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
232	UPDATE	imiH	 carbapenem;  CphA beta-lactamase;  antibiotic inactivation; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
233	UPDATE	LEN-21	 penam;  LEN beta-lactamase;  antibiotic inactivation;  penem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2462	UPDATE	Cutibacterium acnes gyrA conferring resistance to fluoroquinolones	 levofloxacin;  antibiotic target alteration;  fluoroquinolone antibiotic;  fluoroquinolone resistant gyrA;  ciprofloxacin; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
UPDATED category_aro_name with levofloxacin
UPDATED category_aro_cvterm_id with 35988
UPDATED category_aro_accession with 0000071
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.
UPDATED category_aro_name with ciprofloxacin
UPDATED category_aro_cvterm_id with 35954
UPDATED category_aro_accession with 0000036
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
"
2228	UPDATE	PEDO-1	 carbapenem;  antibiotic inactivation;  subclass B3 PEDO beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2229	UPDATE	PEDO-2	 carbapenem;  antibiotic inactivation;  subclass B3 PEDO beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2227	UPDATE	VCC-1	 carbapenem;  monobactam;  VCC beta-lactamase;  antibiotic inactivation;  penam; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2224	UPDATE	Pseudomonas aeruginosa oprD with mutation conferring resistance to imipenem	 penam;  carbapenem;  imipenem;  penem;  reduced permeability to antibiotic;  Outer Membrane Porin (Opr);  cephalosporin;  cephamycin;  monobactam; 	model_description; model_param	"UPDATED model_description with Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
"
992	UPDATE	SHV-66	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  SHV beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2222	UPDATE	VEB-1b	 antibiotic inactivation;  monobactam;  cephalosporin;  VEB beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2223	UPDATE	MexZ	 erythromycin;  arbekacin;  tetracycline antibiotic;  meropenem;  antibiotic efflux;  resistance-nodulation-cell division (RND) antibiotic efflux pump;  ofloxacin;  norfloxacin;  macrolide antibiotic;  carbapenem;  cephalosporin;  ciprofloxacin;  gentamicin C;  amikacin;  aminoglycoside antibiotic;  disinfecting agents and antiseptics;  protein(s) and two-component regulatory system modulating antibiotic efflux;  penam;  efflux pump complex or subunit conferring antibiotic resistance;  cephamycin;  acriflavine;  fluoroquinolone antibiotic;  chloramphenicol;  phenicol antibiotic;  tetracycline;  tobramycin; 	model_description; model_param	"UPDATED model_description with Protein Overexpression Models (POM) are similar to Protein Variant Models (PVM) in that they include a protein reference sequence, a curated BLASTP bitscore cut-off, and mapped resistance variants. Whereas PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, reporting only those with curated mutations conferring AMR, POMs are restricted to regulatory proteins and report both wild-type sequences and/or sequences with mutations leading to overexpression of efflux complexes. The former lead to efflux of antibiotics at basal levels, while the latter can confer clinical resistance. POMs include a protein reference sequence (often from wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Perfect RGI match is 100% identical to the wild-type reference protein sequence along its entire length, a Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value may or may not contain at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off may or may not contain at least one curated mutation from amongst the mapped resistance variants.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
"
1	UPDATE	PDC-4	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2705	UPDATE	MexEF-OprN with MexS mutations conferring resistance to chloramphenicol, ciprofloxacin, and trimethoprim	 antibiotic efflux;  resistance-nodulation-cell division (RND) antibiotic efflux pump;  trimethoprim;  efflux pump complex or subunit conferring antibiotic resistance;  diaminopyrimidine antibiotic;  ciprofloxacin;  fluoroquinolone antibiotic;  phenicol antibiotic;  chloramphenicol; 	model_description; model_param	"UPDATED model_description with Efflux Pump System Meta-Models (EPS) are dedicated to efflux complexes and their regulators, such as AcrAB-TolC. Using the efflux pump components parameter, this model type simply includes a list of detection models for each component of the complex. This model type is still under development and not currently supported by the Resistance Gene Identifier (RGI) software.
UPDATED param_description with Association of proteins within efflux protein complexes or regulatory networks are encoded by the efflux pump components parameter: model_id,model_id,model_id, etc.
"
1433	UPDATE	CMY-18	 antibiotic inactivation;  CMY beta-lactamase;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
133	UPDATE	arr-8	 antibiotic inactivation;  rifampin;  rifapentine;  rifabutin;  rifampin ADP-ribosyltransferase (Arr);  rifaximin;  rifamycin antibiotic; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4881	UPDATE	OXA-552	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2707	UPDATE	MexEF-OprN with MvaT deletion conferring resistance to chloramphenicol and norfloxacin	 antibiotic efflux;  resistance-nodulation-cell division (RND) antibiotic efflux pump;  norfloxacin;  trimethoprim;  efflux pump complex or subunit conferring antibiotic resistance;  diaminopyrimidine antibiotic;  fluoroquinolone antibiotic;  phenicol antibiotic;  chloramphenicol; 	model_description; model_param	"UPDATED model_description with Efflux Pump System Meta-Models (EPS) are dedicated to efflux complexes and their regulators, such as AcrAB-TolC. Using the efflux pump components parameter, this model type simply includes a list of detection models for each component of the complex. This model type is still under development and not currently supported by the Resistance Gene Identifier (RGI) software.
UPDATED param_description with Association of proteins within efflux protein complexes or regulatory networks are encoded by the efflux pump components parameter: model_id,model_id,model_id, etc.
"
146	UPDATE	OXA-98	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5458	UPDATE	PDC-329	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
144	UPDATE	IMP-12	 penam;  antibiotic inactivation;  penem;  carbapenem;  cephalosporin;  IMP beta-lactamase;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
145	UPDATE	OXA-229	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
142	UPDATE	tet(E)	 tetracycline antibiotic;  efflux pump complex or subunit conferring antibiotic resistance;  major facilitator superfamily (MFS) antibiotic efflux pump;  tetracycline;  antibiotic efflux; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
143	UPDATE	cphA7	 carbapenem;  CphA beta-lactamase;  antibiotic inactivation; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
140	UPDATE	AAC(6')-IIb	 antibiotic inactivation;  AAC(6');  kanamycin A;  aminoglycoside antibiotic;  gentamicin A;  tobramycin; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with kanamycin A
UPDATED category_aro_cvterm_id with 35966
UPDATED category_aro_accession with 0000049
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.
UPDATED category_aro_name with gentamicin A
UPDATED category_aro_cvterm_id with 40942
UPDATED category_aro_accession with 3004015
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Gentamicin A is part of a complex of broad spectrum aminoglycoside antibiotics. Gentamicin inhibits protein synthesis, resulting in bacterial cell death.
UPDATED category_aro_name with tobramycin
UPDATED category_aro_cvterm_id with 35969
UPDATED category_aro_accession with 0000052
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5459	UPDATE	PDC-33	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4884	UPDATE	OXA-555	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1052	UPDATE	OXA-206	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
148	UPDATE	SHV-92	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  SHV beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
149	UPDATE	aadA12	 antibiotic inactivation;  aminoglycoside antibiotic;  ANT(3'');  streptomycin;  spectinomycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4505	UPDATE	CTX-M-176	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4504	UPDATE	CTX-M-175	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4507	UPDATE	CTX-M-178	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4506	UPDATE	CTX-M-177	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4501	UPDATE	CTX-M-172	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4500	UPDATE	CTX-M-171	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4503	UPDATE	CTX-M-174	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4502	UPDATE	CTX-M-173	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4509	UPDATE	CTX-M-180	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4508	UPDATE	CTX-M-179	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1055	UPDATE	Escherichia coli parE conferring resistance to fluoroquinolones	 fluoroquinolone resistant parE;  grepafloxacin;  trovafloxacin;  ofloxacin;  norfloxacin;  nalidixic acid;  lomefloxacin;  gatifloxacin;  levofloxacin;  sparfloxacin;  antibiotic target alteration;  enoxacin;  ciprofloxacin;  pefloxacin;  fluoroquinolone antibiotic;  moxifloxacin; 	model_description; model_param	"UPDATED model_description with Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
"
120	UPDATE	aadA4	 antibiotic inactivation;  aminoglycoside antibiotic;  ANT(3'');  streptomycin;  spectinomycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2088	UPDATE	Mycolicibacterium smegmatis 16S rRNA (rrsB) mutation conferring resistance to streptomycin	 antibiotic target alteration;  streptomycin;  aminoglycoside antibiotic;  16s rRNA with mutation conferring resistance to aminoglycoside antibiotics; 	model_description; model_param	"UPDATED model_description with Ribosomal RNA (rRNA) Gene Variant Models (RVM) are similar to Protein Variant Models (PVM), i.e. detect  sequences based on their similarity to a curated reference sequence and secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles, except RVMs are designed to detect AMR acquired via mutation of genes encoding ribosomal RNAs (rRNA). RVMs include a rRNA reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTN bit-score above the curated BLASTN cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTN bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
UPDATED param_description with The BLASTN bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
"
1056	UPDATE	VIM-19	 penam;  antibiotic inactivation;  penem;  carbapenem;  cephalosporin;  cephamycin;  VIM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
121	UPDATE	mdtF	 penam;  antibiotic efflux;  resistance-nodulation-cell division (RND) antibiotic efflux pump;  norfloxacin;  macrolide antibiotic;  efflux pump complex or subunit conferring antibiotic resistance;  oxacillin;  cloxacillin;  fluoroquinolone antibiotic;  erythromycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1989	UPDATE	Klebsiella pneumoniae acrR with mutation conferring multidrug antibiotic resistance	 penam;  antibiotic efflux;  triclosan;  rifampin;  resistance-nodulation-cell division (RND) antibiotic efflux pump;  protein(s) and two-component regulatory system modulating antibiotic efflux;  efflux pump complex or subunit conferring antibiotic resistance;  antibiotic target alteration;  disinfecting agents and antiseptics;  tetracycline antibiotic;  cephalosporin;  cefalotin;  tigecycline;  glycylcycline;  ampicillin;  fluoroquinolone antibiotic;  rifamycin antibiotic;  phenicol antibiotic;  tetracycline;  chloramphenicol; 	model_description; model_param	"UPDATED model_description with Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
"
2083	UPDATE	Mycoplasma hominis parC conferring resistance to fluoroquinolones	 grepafloxacin;  trovafloxacin;  ofloxacin;  norfloxacin;  nalidixic acid;  lomefloxacin;  gatifloxacin;  sparfloxacin;  levofloxacin;  fluoroquinolone resistant parC;  antibiotic target alteration;  enoxacin;  ciprofloxacin;  pefloxacin;  fluoroquinolone antibiotic;  moxifloxacin; 	model_description; model_param	"UPDATED model_description with Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
"
2080	UPDATE	Escherichia coli 16S rRNA (rrsH) mutation conferring resistance to spectinomycin	 antibiotic target alteration;  aminoglycoside antibiotic;  spectinomycin;  16s rRNA with mutation conferring resistance to aminoglycoside antibiotics; 	model_description; model_param	"UPDATED model_description with Ribosomal RNA (rRNA) Gene Variant Models (RVM) are similar to Protein Variant Models (PVM), i.e. detect  sequences based on their similarity to a curated reference sequence and secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles, except RVMs are designed to detect AMR acquired via mutation of genes encoding ribosomal RNAs (rRNA). RVMs include a rRNA reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTN bit-score above the curated BLASTN cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTN bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
UPDATED param_description with The BLASTN bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
"
2081	UPDATE	patA	 antibiotic efflux;  ATP-binding cassette (ABC) antibiotic efflux pump;  norfloxacin;  efflux pump complex or subunit conferring antibiotic resistance;  ciprofloxacin;  fluoroquinolone antibiotic; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2086	UPDATE	Escherichia coli 16S rRNA (rrnB) mutation conferring resistance to tetracycline	 tetracycline antibiotic;  antibiotic target alteration;  16S rRNA with mutation conferring resistance to tetracycline derivatives;  tetracycline; 	model_description; model_param	"UPDATED model_description with Ribosomal RNA (rRNA) Gene Variant Models (RVM) are similar to Protein Variant Models (PVM), i.e. detect  sequences based on their similarity to a curated reference sequence and secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles, except RVMs are designed to detect AMR acquired via mutation of genes encoding ribosomal RNAs (rRNA). RVMs include a rRNA reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTN bit-score above the curated BLASTN cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTN bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
UPDATED param_description with The BLASTN bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
"
2087	UPDATE	aadA13	 antibiotic inactivation;  aminoglycoside antibiotic;  ANT(3'');  streptomycin;  spectinomycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2084	UPDATE	Mycobacteroides abscessus 16S rRNA mutation conferring resistance to amikacin	 antibiotic target alteration;  amikacin;  aminoglycoside antibiotic;  16s rRNA with mutation conferring resistance to aminoglycoside antibiotics; 	model_description; model_param	"UPDATED model_description with Ribosomal RNA (rRNA) Gene Variant Models (RVM) are similar to Protein Variant Models (PVM), i.e. detect  sequences based on their similarity to a curated reference sequence and secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles, except RVMs are designed to detect AMR acquired via mutation of genes encoding ribosomal RNAs (rRNA). RVMs include a rRNA reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTN bit-score above the curated BLASTN cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTN bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
UPDATED param_description with The BLASTN bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
"
2085	UPDATE	Escherichia coli 16S rRNA (rrnB) mutation conferring resistance to spectinomycin	 antibiotic target alteration;  aminoglycoside antibiotic;  spectinomycin;  16s rRNA with mutation conferring resistance to aminoglycoside antibiotics; 	model_description; model_param	"UPDATED model_description with Ribosomal RNA (rRNA) Gene Variant Models (RVM) are similar to Protein Variant Models (PVM), i.e. detect  sequences based on their similarity to a curated reference sequence and secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles, except RVMs are designed to detect AMR acquired via mutation of genes encoding ribosomal RNAs (rRNA). RVMs include a rRNA reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTN bit-score above the curated BLASTN cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTN bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
UPDATED param_description with The BLASTN bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
"
5328	UPDATE	PDC-189	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3342	UPDATE	dfrA3b	 trimethoprim;  diaminopyrimidine antibiotic;  trimethoprim resistant dihydrofolate reductase dfr;  antibiotic target replacement; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3882	UPDATE	PDC-41	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5451	UPDATE	PDC-320	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
124	UPDATE	IND-7	 carbapenem;  antibiotic inactivation;  IND beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3340	UPDATE	aacA43	 AAC(6');  kanamycin A;  antibiotic inactivation;  aminoglycoside antibiotic;  tobramycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2712	UPDATE	MexXY-OprA	 antibiotic efflux;  tobramycin;  resistance-nodulation-cell division (RND) antibiotic efflux pump;  ofloxacin;  norfloxacin;  meropenem;  macrolide antibiotic;  carbapenem;  efflux pump complex or subunit conferring antibiotic resistance;  arbekacin;  ciprofloxacin;  tetracycline antibiotic;  gentamicin C;  amikacin;  aminoglycoside antibiotic;  fluoroquinolone antibiotic;  tetracycline;  erythromycin; 	model_description; model_param	"UPDATED model_description with Efflux Pump System Meta-Models (EPS) are dedicated to efflux complexes and their regulators, such as AcrAB-TolC. Using the efflux pump components parameter, this model type simply includes a list of detection models for each component of the complex. This model type is still under development and not currently supported by the Resistance Gene Identifier (RGI) software.
UPDATED param_description with Association of proteins within efflux protein complexes or regulatory networks are encoded by the efflux pump components parameter: model_id,model_id,model_id, etc.
"
2713	UPDATE	MexXY-OprM	 erythromycin;  tetracycline antibiotic;  meropenem;  antibiotic efflux;  resistance-nodulation-cell division (RND) antibiotic efflux pump;  ofloxacin;  norfloxacin;  macrolide antibiotic;  carbapenem;  cephalosporin;  ciprofloxacin;  gentamicin C;  amikacin;  aminoglycoside antibiotic;  disinfecting agents and antiseptics;  penam;  efflux pump complex or subunit conferring antibiotic resistance;  cephamycin;  acriflavine;  fluoroquinolone antibiotic;  chloramphenicol;  phenicol antibiotic;  tetracycline;  tobramycin; 	model_description; model_param	"UPDATED model_description with Efflux Pump System Meta-Models (EPS) are dedicated to efflux complexes and their regulators, such as AcrAB-TolC. Using the efflux pump components parameter, this model type simply includes a list of detection models for each component of the complex. This model type is still under development and not currently supported by the Resistance Gene Identifier (RGI) software.
UPDATED param_description with Association of proteins within efflux protein complexes or regulatory networks are encoded by the efflux pump components parameter: model_id,model_id,model_id, etc.
"
3341	UPDATE	Erm(K)	 Erm 23S ribosomal RNA methyltransferase;  macrolide antibiotic;  antibiotic target alteration;  streptogramin antibiotic;  erythromycin;  lincosamide antibiotic; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with erythromycin
UPDATED category_aro_cvterm_id with 35925
UPDATED category_aro_accession with 0000006
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure/function processes critical for life or replication are inhibited.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2716	UPDATE	OpmB	 kitasamycin;  resistance-nodulation-cell division (RND) antibiotic efflux pump;  rokitamycin;  aztreonam;  aminocoumarin antibiotic;  novobiocin;  macrolide antibiotic;  antibiotic efflux;  efflux pump complex or subunit conferring antibiotic resistance;  tetracycline antibiotic;  monobactam;  tetracycline;  erythromycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2717	UPDATE	MuxA	 kitasamycin;  resistance-nodulation-cell division (RND) antibiotic efflux pump;  rokitamycin;  aztreonam;  aminocoumarin antibiotic;  novobiocin;  macrolide antibiotic;  antibiotic efflux;  efflux pump complex or subunit conferring antibiotic resistance;  tetracycline antibiotic;  monobactam;  tetracycline;  erythromycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3346	UPDATE	AQU-2	 antibiotic inactivation;  AQU beta-lactamase;  cephalosporin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2718	UPDATE	MuxB	 kitasamycin;  resistance-nodulation-cell division (RND) antibiotic efflux pump;  rokitamycin;  aztreonam;  aminocoumarin antibiotic;  novobiocin;  macrolide antibiotic;  antibiotic efflux;  efflux pump complex or subunit conferring antibiotic resistance;  tetracycline antibiotic;  monobactam;  tetracycline;  erythromycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
127	UPDATE	clbB	 dalfopristin;  thiamphenicol;  oxazolidinone antibiotic;  virginiamycin M1;  pleuromutilin antibiotic;  tiamulin;  madumycin II;  griseoviridin;  streptogramin A antibiotic;  lincomycin;  streptogramin antibiotic;  antibiotic target alteration;  lincosamide antibiotic;  azidamfenicol;  clindamycin;  phenicol antibiotic;  Cfr 23S ribosomal RNA methyltransferase;  chloramphenicol; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3347	UPDATE	AQU-3	 antibiotic inactivation;  AQU beta-lactamase;  cephalosporin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
128	UPDATE	srmB	 Miscellaneous ABC-F subfamily ATP-binding cassette ribosomal protection proteins;  spiramycin;  antibiotic target protection;  macrolide antibiotic; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5078	UPDATE	OXA-769	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5079	UPDATE	OXA-770	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3344	UPDATE	dfrI	 trimethoprim;  diaminopyrimidine antibiotic;  trimethoprim resistant dihydrofolate reductase dfr;  antibiotic target replacement; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
129	UPDATE	FosX	 fosfomycin;  fosfomycin thiol transferase;  antibiotic inactivation;  phosphonic acid antibiotic; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_name with phosphonic acid antibiotic
UPDATED category_aro_cvterm_id with 45731
UPDATED category_aro_accession with 3007149
UPDATED category_aro_class_name with Drug Class
UPDATED category_aro_description with A group of antibiotics derived from phosphonic acids.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5072	UPDATE	OXA-763	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5073	UPDATE	OXA-764	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5070	UPDATE	OXA-761	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5071	UPDATE	OXA-762	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5076	UPDATE	OXA-767	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5077	UPDATE	OXA-768	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5074	UPDATE	OXA-765	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5075	UPDATE	OXA-766	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1832	UPDATE	QnrS2	 sparfloxacin;  norfloxacin;  quinolone resistance protein (qnr);  gatifloxacin;  levofloxacin;  antibiotic target protection;  ciprofloxacin;  fluoroquinolone antibiotic;  nalidixic acid;  moxifloxacin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1833	UPDATE	OXA-374	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1830	UPDATE	APH(3'')-Ib	 antibiotic inactivation;  APH(3'');  streptomycin;  aminoglycoside antibiotic; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1831	UPDATE	AAC(6')-Iid	 AAC(6');  antibiotic inactivation;  aminoglycoside antibiotic; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1836	UPDATE	OXA-201	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3798	UPDATE	tet(X5)	 antibiotic inactivation;  oxytetracycline;  tetracycline antibiotic;  minocycline;  tetracycline inactivation enzyme;  tetracycline; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with minocycline
UPDATED category_aro_cvterm_id with 36291
UPDATED category_aro_accession with 3000152
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Minocycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.
UPDATED category_aro_name with oxytetracycline
UPDATED category_aro_cvterm_id with 37012
UPDATED category_aro_accession with 3000668
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Oxytetracycline is a derivative of tetracycline with a 5-hydroxyl group. Its activity is similar to other tetracyclines.
UPDATED category_aro_name with tetracycline
UPDATED category_aro_cvterm_id with 35968
UPDATED category_aro_accession with 0000051
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1834	UPDATE	TEM-94	 penam;  antibiotic inactivation;  penem;  cephalosporin;  monobactam;  ampicillin;  TEM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1835	UPDATE	tet(38)	 tetracycline antibiotic;  efflux pump complex or subunit conferring antibiotic resistance;  major facilitator superfamily (MFS) antibiotic efflux pump;  tetracycline;  antibiotic efflux; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3795	UPDATE	ArnT	 pmr phosphoethanolamine transferase;  peptide antibiotic;  antibiotic target alteration;  colistin B;  colistin A; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with colistin B
UPDATED category_aro_cvterm_id with 36968
UPDATED category_aro_accession with 3000624
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.
UPDATED category_aro_name with colistin A
UPDATED category_aro_cvterm_id with 36966
UPDATED category_aro_accession with 3000622
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3794	UPDATE	LpsA	 peptide antibiotic;  reduced permeability to antibiotic;  Intrinsic peptide antibiotic resistant Lps;  polymyxin B;  defensin; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with polymyxin B
UPDATED category_aro_cvterm_id with 36593
UPDATED category_aro_accession with 3000454
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Polymyxin B is mixture of mostly polymyxins B1 and B2, mainly used for resistant gram-negative infections. They are polypeptides with cationic detergent action on cell membranes.
UPDATED category_aro_name with defensin
UPDATED category_aro_cvterm_id with 37037
UPDATED category_aro_accession with 3000693
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Defensins are natural cationic peptides that have antibiotic properties. It is part of the innate immune system of plants and animals.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3797	UPDATE	tet(X6)	 antibiotic inactivation;  oxytetracycline;  tetracycline antibiotic;  minocycline;  tetracycline inactivation enzyme;  tetracycline; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with minocycline
UPDATED category_aro_cvterm_id with 36291
UPDATED category_aro_accession with 3000152
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Minocycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.
UPDATED category_aro_name with oxytetracycline
UPDATED category_aro_cvterm_id with 37012
UPDATED category_aro_accession with 3000668
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Oxytetracycline is a derivative of tetracycline with a 5-hydroxyl group. Its activity is similar to other tetracyclines.
UPDATED category_aro_name with tetracycline
UPDATED category_aro_cvterm_id with 35968
UPDATED category_aro_accession with 0000051
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1839	UPDATE	aadA14	 antibiotic inactivation;  aminoglycoside antibiotic;  ANT(3'');  streptomycin;  spectinomycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3791	UPDATE	eptB	 colistin B;  polymyxin B;  pmr phosphoethanolamine transferase;  colistin A;  peptide antibiotic;  antibiotic target alteration; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with colistin B
UPDATED category_aro_cvterm_id with 36968
UPDATED category_aro_accession with 3000624
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.
UPDATED category_aro_name with polymyxin B
UPDATED category_aro_cvterm_id with 36593
UPDATED category_aro_accession with 3000454
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Polymyxin B is mixture of mostly polymyxins B1 and B2, mainly used for resistant gram-negative infections. They are polypeptides with cationic detergent action on cell membranes.
UPDATED category_aro_name with colistin A
UPDATED category_aro_cvterm_id with 36966
UPDATED category_aro_accession with 3000622
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3790	UPDATE	MecC-type methicillin resistance repressor MecI	 penam;  methicillin resistant PBP2;  methicillin;  antibiotic target replacement; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with methicillin
UPDATED category_aro_cvterm_id with 35934
UPDATED category_aro_accession with 0000015
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Derived from penicillin to combat penicillin-resistance, methicillin is insensitive to beta-lactamases (also known as penicillinases) secreted by many penicillin-resistant bacteria. Methicillin is bactericidal, and acts by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3793	UPDATE	LpsB	 reduced permeability to antibiotic;  colistin B;  defensin;  Intrinsic peptide antibiotic resistant Lps;  colistin A;  peptide antibiotic; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with colistin B
UPDATED category_aro_cvterm_id with 36968
UPDATED category_aro_accession with 3000624
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.
UPDATED category_aro_name with defensin
UPDATED category_aro_cvterm_id with 37037
UPDATED category_aro_accession with 3000693
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Defensins are natural cationic peptides that have antibiotic properties. It is part of the innate immune system of plants and animals.
UPDATED category_aro_name with colistin A
UPDATED category_aro_cvterm_id with 36966
UPDATED category_aro_accession with 3000622
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3792	UPDATE	CrcB	 aminoglycoside antibiotic;  antibiotic efflux;  multidrug and toxic compound extrusion (MATE) transporter;  efflux pump complex or subunit conferring antibiotic resistance; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4981	UPDATE	OXA-661	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2155	UPDATE	Cutibacterium acnes 16S rRNA mutation conferring resistance to tetracycline	 tetracycline antibiotic;  antibiotic target alteration;  16S rRNA with mutation conferring resistance to tetracycline derivatives;  tetracycline; 	model_description; model_param	"UPDATED model_description with Ribosomal RNA (rRNA) Gene Variant Models (RVM) are similar to Protein Variant Models (PVM), i.e. detect  sequences based on their similarity to a curated reference sequence and secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles, except RVMs are designed to detect AMR acquired via mutation of genes encoding ribosomal RNAs (rRNA). RVMs include a rRNA reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTN bit-score above the curated BLASTN cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTN bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
UPDATED param_description with The BLASTN bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
"
2404	UPDATE	Neisseria gonorrhoeae gyrA conferring resistance to fluoroquinolones	 antibiotic target alteration;  fluoroquinolone antibiotic;  fluoroquinolone resistant gyrA;  ciprofloxacin; 	model_description; model_param	"UPDATED model_description with Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
"
2405	UPDATE	Neisseria gonorrhoeae parC conferring resistance to fluoroquinolones	 antibiotic target alteration;  fluoroquinolone resistant parC;  fluoroquinolone antibiotic;  ciprofloxacin; 	model_description; model_param	"UPDATED model_description with Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
"
4985	UPDATE	OXA-669	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2403	UPDATE	Salmonella enterica gyrA conferring resistance to fluoroquinolones	 antibiotic target alteration;  nalidixic acid;  fluoroquinolone antibiotic;  fluoroquinolone resistant gyrA;  ciprofloxacin; 	model_description; model_param	"UPDATED model_description with Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
"
4987	UPDATE	OXA-674	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4986	UPDATE	OXA-670	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4989	UPDATE	OXA-676	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4988	UPDATE	OXA-675	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
931	UPDATE	OXA-316	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2158	UPDATE	Escherichia coli EF-Tu mutants conferring resistance to Pulvomycin	 antibiotic target alteration;  elfamycin antibiotic;  pulvomycin;  elfamycin resistant EF-Tu; 	model_description; model_param	"UPDATED model_description with Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
"
936	UPDATE	OKP-A-13	 penam;  antibiotic inactivation;  OKP beta-lactamase;  cephalosporin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
935	UPDATE	OXA-314	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
934	UPDATE	IMP-8	 penam;  antibiotic inactivation;  penem;  carbapenem;  cephalosporin;  IMP beta-lactamase;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5380	UPDATE	PDC-242	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5381	UPDATE	PDC-243	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5382	UPDATE	PDC-244	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5383	UPDATE	PDC-245	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5384	UPDATE	PDC-246	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5385	UPDATE	PDC-247	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5386	UPDATE	PDC-248	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5387	UPDATE	PDC-249	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5388	UPDATE	PDC-25	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5389	UPDATE	PDC-250	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
136	UPDATE	CMY-9	 antibiotic inactivation;  CMY beta-lactamase;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1955	UPDATE	OXA-29	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1954	UPDATE	TEM-154	 penam;  antibiotic inactivation;  penem;  cephalosporin;  monobactam;  ampicillin;  TEM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1957	UPDATE	VIM-18	 penam;  antibiotic inactivation;  penem;  carbapenem;  cephalosporin;  cephamycin;  VIM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1956	UPDATE	IMI-1	 carbapenem;  antibiotic inactivation;  IMI beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1951	UPDATE	TEM-76	 penam;  antibiotic inactivation;  penem;  cephalosporin;  monobactam;  ampicillin;  TEM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1950	UPDATE	arr-1	 antibiotic inactivation;  rifampin;  rifapentine;  rifabutin;  rifampin ADP-ribosyltransferase (Arr);  rifaximin;  rifamycin antibiotic; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1953	UPDATE	SHV-155	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  SHV beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1952	UPDATE	OXA-1	 penam;  antibiotic inactivation;  cephalosporin;  carbapenem;  piperacillin-tazobactam;  cefalotin;  amoxicillin;  ampicillin;  clavulanic acid;  piperacillin;  tazobactam;  OXA beta-lactamase;  amoxicillin-clavulanic acid; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1829	UPDATE	CMY-87	 antibiotic inactivation;  CMY beta-lactamase;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1959	UPDATE	ACT-7	 antibiotic inactivation;  carbapenem;  penam;  ACT beta-lactamase;  cephalosporin;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1958	UPDATE	VIM-33	 penam;  antibiotic inactivation;  penem;  carbapenem;  cephalosporin;  cephamycin;  VIM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1828	UPDATE	GES-6	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  GES beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
569	UPDATE	OXA-228	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2357	UPDATE	ADC-41	 antibiotic inactivation;  cephalosporin;  ADC beta-lactamase without carbapenemase activity; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
132	UPDATE	TEM-198	 penam;  antibiotic inactivation;  penem;  cephalosporin;  monobactam;  ampicillin;  TEM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
905	UPDATE	CTX-M-93	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1992	UPDATE	dfrA1	 trimethoprim;  diaminopyrimidine antibiotic;  trimethoprim resistant dihydrofolate reductase dfr;  antibiotic target replacement; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1825	UPDATE	CTX-M-27	 penam;  carbapenem;  antibiotic inactivation;  piperacillin-tazobactam;  cephalosporin;  cefazolin;  ceftazidime;  cefalotin;  amoxicillin-clavulanic acid;  amoxicillin;  ampicillin;  clavulanic acid;  piperacillin;  tazobactam;  cefixime;  ertapenem;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
829	UPDATE	DHA-17	 antibiotic inactivation;  cephalosporin;  cephamycin;  DHA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
828	UPDATE	TEM-83	 penam;  antibiotic inactivation;  penem;  cephalosporin;  monobactam;  ampicillin;  TEM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1824	UPDATE	oleI	 antibiotic inactivation;  ole glycosyltransferase;  macrolide antibiotic;  oleandomycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
825	UPDATE	SHV-20	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  SHV beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
824	UPDATE	vanD	 glycopeptide resistance gene cluster;  Van ligase;  teicoplanin;  glycopeptide antibiotic;  antibiotic target alteration;  vancomycin; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with vancomycin
UPDATED category_aro_cvterm_id with 35947
UPDATED category_aro_accession with 0000028
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.
UPDATED category_aro_name with teicoplanin
UPDATED category_aro_cvterm_id with 35948
UPDATED category_aro_accession with 0000029
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Teicoplanin is a glycopeptide antibiotic used in the prophylaxis and treatment of serious infections caused by Gram-positive bacteria. Teicoplanin has a unique acyl-aliphatic chain, and binds to cell wall precursors to inhibit transglycosylation  and transpeptidation.
UPDATED param_value with 350
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
827	UPDATE	QnrB55	 sparfloxacin;  norfloxacin;  quinolone resistance protein (qnr);  gatifloxacin;  levofloxacin;  antibiotic target protection;  ciprofloxacin;  fluoroquinolone antibiotic;  nalidixic acid;  moxifloxacin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
826	UPDATE	TolC	 tetracycline;  erythromycin;  penem;  tetracycline antibiotic;  piperacillin;  antibiotic efflux;  ATP-binding cassette (ABC) antibiotic efflux pump;  major facilitator superfamily (MFS) antibiotic efflux pump;  resistance-nodulation-cell division (RND) antibiotic efflux pump;  norfloxacin;  nalidixic acid;  aminocoumarin antibiotic;  cephalosporin;  macrolide antibiotic;  carbapenem;  ceftazidime;  cefalotin;  spectinomycin;  glycylcycline;  oxacillin;  ciprofloxacin;  cloxacillin;  gentamicin C;  streptomycin;  aminoglycoside antibiotic;  disinfecting agents and antiseptics;  polymyxin B3;  polymyxin B1;  polymyxin B;  rifamycin antibiotic;  imipenem;  peptide antibiotic;  rifampin;  ticarcillin;  ampicillin;  ertapenem;  penam;  triclosan;  novobiocin;  efflux pump complex or subunit conferring antibiotic resistance;  polymyxin B2;  tigecycline;  polymyxin B4;  cephamycin;  fluoroquinolone antibiotic;  tobramycin;  phenicol antibiotic;  azithromycin;  chloramphenicol; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
821	UPDATE	Mycobacterium tuberculosis embB with mutation conferring resistance to rifampicin	 antibiotic target alteration;  rifamycin-resistant arabinosyltransferase;  rifampin;  rifamycin antibiotic; 	model_description; model_param	"UPDATED model_description with Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
"
820	UPDATE	mdtB	 efflux pump complex or subunit conferring antibiotic resistance;  antibiotic efflux;  aminocoumarin antibiotic;  resistance-nodulation-cell division (RND) antibiotic efflux pump;  novobiocin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
822	UPDATE	QnrD1	 sparfloxacin;  norfloxacin;  quinolone resistance protein (qnr);  gatifloxacin;  levofloxacin;  antibiotic target protection;  ciprofloxacin;  fluoroquinolone antibiotic;  nalidixic acid;  moxifloxacin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4259	UPDATE	ADC-194	 antibiotic inactivation;  cephalosporin;  ADC beta-lactamases pending classification for carbapenemase activity; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1826	UPDATE	ykkC	 antibiotic efflux;  small multidrug resistance (SMR) antibiotic efflux pump;  efflux pump complex or subunit conferring antibiotic resistance;  tetracycline antibiotic;  streptomycin;  aminoglycoside antibiotic;  phenicol antibiotic;  tetracycline;  chloramphenicol; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1536	UPDATE	OXA-421	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4258	UPDATE	ADC-193	 antibiotic inactivation;  cephalosporin;  ADC beta-lactamases pending classification for carbapenemase activity; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1821	UPDATE	AAC(6')-Ir	 antibiotic inactivation;  AAC(6');  kanamycin A;  amikacin;  aminoglycoside antibiotic;  tobramycin; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with kanamycin A
UPDATED category_aro_cvterm_id with 35966
UPDATED category_aro_accession with 0000049
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.
UPDATED category_aro_name with amikacin
UPDATED category_aro_cvterm_id with 35932
UPDATED category_aro_accession with 0000013
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.
UPDATED category_aro_name with tobramycin
UPDATED category_aro_cvterm_id with 35969
UPDATED category_aro_accession with 0000052
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
618	UPDATE	emeA	 efflux pump complex or subunit conferring antibiotic resistance;  antibiotic efflux;  multidrug and toxic compound extrusion (MATE) transporter;  acriflavine;  disinfecting agents and antiseptics; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1820	UPDATE	bacA	 peptide antibiotic;  undecaprenyl pyrophosphate related proteins;  bacitracin B;  bacitracin F;  bacitracin A;  antibiotic target alteration;  bacitracin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1483	UPDATE	AAC(3)-Xa	 kanamycin A;  antibiotic inactivation;  AAC(3);  aminoglycoside antibiotic; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1482	UPDATE	SME-1	 carbapenem;  antibiotic inactivation;  SME beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1481	UPDATE	OXY-1-4	 penam;  OXY beta-lactamase;  cephalosporin;  antibiotic inactivation;  monobactam; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1480	UPDATE	EXO-1	 penam;  antibiotic inactivation;  EXO beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5498	UPDATE	PDC-368	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5499	UPDATE	PDC-369	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1485	UPDATE	MOX-8	 penam;  antibiotic inactivation;  MOX beta-lactamase;  cephamycin;  cephalosporin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1484	UPDATE	ACT-27	 antibiotic inactivation;  carbapenem;  penam;  ACT beta-lactamase;  cephalosporin;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5494	UPDATE	PDC-364	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5495	UPDATE	PDC-365	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5496	UPDATE	PDC-366	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5497	UPDATE	PDC-367	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3302	UPDATE	tet(56)	 tetracycline antibiotic;  antibiotic inactivation;  tetracycline inactivation enzyme;  oxytetracycline;  tetracycline; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with oxytetracycline
UPDATED category_aro_cvterm_id with 37012
UPDATED category_aro_accession with 3000668
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Oxytetracycline is a derivative of tetracycline with a 5-hydroxyl group. Its activity is similar to other tetracyclines.
UPDATED category_aro_name with tetracycline
UPDATED category_aro_cvterm_id with 35968
UPDATED category_aro_accession with 0000051
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3303	UPDATE	ermZ	 Erm 23S ribosomal RNA methyltransferase;  macrolide antibiotic;  antibiotic target alteration;  streptogramin antibiotic;  spiramycin;  lincosamide antibiotic; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with spiramycin
UPDATED category_aro_cvterm_id with 36295
UPDATED category_aro_accession with 3000156
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Spiramycin is a 16-membered macrolide and is natural product produced by Streptomyces ambofaciens. It binds to the 50S subunit of bacterial ribosomes and inhibits peptidyl transfer activity to disrupt protein synthesis.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5492	UPDATE	PDC-362	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3301	UPDATE	LnuP	 antibiotic inactivation;  lincosamide nucleotidyltransferase (LNU);  lincomycin;  lincosamide antibiotic; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with lincomycin
UPDATED category_aro_cvterm_id with 35964
UPDATED category_aro_accession with 0000046
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Lincomycin is a lincosamide antibiotic that comes from the actinomyces Streptomyces lincolnensis. It binds to the 23s portion of the 50S subunit of bacterial ribosomes and inhibit early elongation of peptide chain by inhibiting transpeptidase reaction.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1713	UPDATE	vanY gene in vanM cluster	 glycopeptide resistance gene cluster;  teicoplanin;  vanY;  glycopeptide antibiotic;  antibiotic target alteration;  vancomycin; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with vancomycin
UPDATED category_aro_cvterm_id with 35947
UPDATED category_aro_accession with 0000028
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.
UPDATED category_aro_name with teicoplanin
UPDATED category_aro_cvterm_id with 35948
UPDATED category_aro_accession with 0000029
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Teicoplanin is a glycopeptide antibiotic used in the prophylaxis and treatment of serious infections caused by Gram-positive bacteria. Teicoplanin has a unique acyl-aliphatic chain, and binds to cell wall precursors to inhibit transglycosylation  and transpeptidation.
UPDATED param_value with 50
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1712	UPDATE	IMP-41	 penam;  antibiotic inactivation;  penem;  carbapenem;  cephalosporin;  IMP beta-lactamase;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5250	UPDATE	PDC-112	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
794	UPDATE	Staphylococcus aureus rpoC conferring resistance to daptomycin	 peptide antibiotic;  antibiotic target alteration;  daptomycin-resistant beta prime subunit of RNA polymerase (rpoC);  daptomycin; 	model_description; model_param	"UPDATED model_description with Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
"
793	UPDATE	IMP-34	 penam;  antibiotic inactivation;  penem;  carbapenem;  cephalosporin;  IMP beta-lactamase;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5257	UPDATE	PDC-121	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
791	UPDATE	SHV-14	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  SHV beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5255	UPDATE	PDC-12	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1719	UPDATE	ceoA	 efflux pump complex or subunit conferring antibiotic resistance;  fluoroquinolone antibiotic;  aminoglycoside antibiotic;  resistance-nodulation-cell division (RND) antibiotic efflux pump;  antibiotic efflux; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5259	UPDATE	PDC-123	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2798	UPDATE	AxyZ	 antibiotic efflux;  resistance-nodulation-cell division (RND) antibiotic efflux pump;  protein(s) and two-component regulatory system modulating antibiotic efflux;  macrolide antibiotic;  efflux pump complex or subunit conferring antibiotic resistance;  cephalosporin;  cefepime;  antibiotic target alteration;  fluoroquinolone antibiotic;  aminoglycoside antibiotic;  erythromycin; 	model_description; model_param	"UPDATED model_description with Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
"
799	UPDATE	CTX-M-31	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
798	UPDATE	cmeC	 antibiotic efflux;  resistance-nodulation-cell division (RND) antibiotic efflux pump;  macrolide antibiotic;  cefotaxime;  efflux pump complex or subunit conferring antibiotic resistance;  cephalosporin;  fusidane antibiotic;  fusidic acid;  fluoroquinolone antibiotic;  erythromycin; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_name with fusidane antibiotic
UPDATED category_aro_cvterm_id with 45735
UPDATED category_aro_accession with 3007153
UPDATED category_aro_class_name with Drug Class
UPDATED category_aro_description with A group of antibiotics possessing steroid rings or steroid-like structures.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1270	UPDATE	QnrS3	 sparfloxacin;  norfloxacin;  quinolone resistance protein (qnr);  gatifloxacin;  levofloxacin;  antibiotic target protection;  ciprofloxacin;  fluoroquinolone antibiotic;  nalidixic acid;  moxifloxacin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2412	UPDATE	Shigella flexneri parC conferring resistance to fluoroquinolones	 antibiotic target alteration;  fluoroquinolone resistant parC;  nalidixic acid;  fluoroquinolone antibiotic;  norfloxacin; 	model_description; model_param	"UPDATED model_description with Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
"
4399	UPDATE	BlaB-38	 carbapenem;  penam;  antibiotic inactivation;  BlaB beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1271	UPDATE	AAC(6')-Iw	 antibiotic inactivation;  AAC(6');  kanamycin A;  amikacin;  aminoglycoside antibiotic;  tobramycin; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with kanamycin A
UPDATED category_aro_cvterm_id with 35966
UPDATED category_aro_accession with 0000049
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.
UPDATED category_aro_name with amikacin
UPDATED category_aro_cvterm_id with 35932
UPDATED category_aro_accession with 0000013
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.
UPDATED category_aro_name with tobramycin
UPDATED category_aro_cvterm_id with 35969
UPDATED category_aro_accession with 0000052
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2143	UPDATE	Borreliella burgdorferi 16S rRNA mutation conferring resistance to gentamicin	 antibiotic target alteration;  gentamicin C;  aminoglycoside antibiotic;  16s rRNA with mutation conferring resistance to aminoglycoside antibiotics; 	model_description; model_param	"UPDATED model_description with Ribosomal RNA (rRNA) Gene Variant Models (RVM) are similar to Protein Variant Models (PVM), i.e. detect  sequences based on their similarity to a curated reference sequence and secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles, except RVMs are designed to detect AMR acquired via mutation of genes encoding ribosomal RNAs (rRNA). RVMs include a rRNA reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTN bit-score above the curated BLASTN cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTN bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
UPDATED param_description with The BLASTN bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
"
1290	UPDATE	TEM-141	 penam;  antibiotic inactivation;  penem;  cephalosporin;  monobactam;  ampicillin;  TEM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
610	UPDATE	SHV-153	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  SHV beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1715	UPDATE	OXA-73	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2142	UPDATE	Mycolicibacterium smegmatis 16S rRNA (rrsA) mutation conferring resistance to viomycin	 peptide antibiotic;  antibiotic target alteration;  16s rRNA with mutation conferring resistance to peptide antibiotics;  viomycin; 	model_description; model_param	"UPDATED model_description with Ribosomal RNA (rRNA) Gene Variant Models (RVM) are similar to Protein Variant Models (PVM), i.e. detect  sequences based on their similarity to a curated reference sequence and secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles, except RVMs are designed to detect AMR acquired via mutation of genes encoding ribosomal RNAs (rRNA). RVMs include a rRNA reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTN bit-score above the curated BLASTN cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTN bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
UPDATED param_description with The BLASTN bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
"
1139	UPDATE	dfrA12	 trimethoprim;  diaminopyrimidine antibiotic;  trimethoprim resistant dihydrofolate reductase dfr;  antibiotic target replacement; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1138	UPDATE	tet(D)	 tetracycline antibiotic;  efflux pump complex or subunit conferring antibiotic resistance;  major facilitator superfamily (MFS) antibiotic efflux pump;  tetracycline;  antibiotic efflux; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
137	UPDATE	APH(2'')-Ie	 antibiotic inactivation;  kanamycin A;  gentamicin B;  aminoglycoside antibiotic;  sisomicin;  arbekacin;  APH(2'');  netilmicin;  gentamicin C;  amikacin;  isepamicin;  gentamicin A;  tobramycin; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with gentamicin A
UPDATED category_aro_cvterm_id with 40942
UPDATED category_aro_accession with 3004015
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Gentamicin A is part of a complex of broad spectrum aminoglycoside antibiotics. Gentamicin inhibits protein synthesis, resulting in bacterial cell death.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1133	UPDATE	SHV-109	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  SHV beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1995	UPDATE	AAC(6')-Iz	 AAC(6');  antibiotic inactivation;  aminoglycoside antibiotic;  tobramycin; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with tobramycin
UPDATED category_aro_cvterm_id with 35969
UPDATED category_aro_accession with 0000052
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1131	UPDATE	AAC(3)-Ic	 antibiotic inactivation;  AAC(3);  sisomicin;  gentamicin B;  gentamicin C;  aminoglycoside antibiotic; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1130	UPDATE	PDC-9	 antibiotic inactivation;  cephalosporin;  carbapenem;  ceftazidime;  PDC beta-lactamase;  monobactam; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1137	UPDATE	TEM-90	 penam;  antibiotic inactivation;  penem;  cephalosporin;  monobactam;  ampicillin;  TEM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1136	UPDATE	MIR-6	 antibiotic inactivation;  monobactam;  cephalosporin;  MIR beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1135	UPDATE	Staphylococcus aureus parE conferring resistance to aminocoumarin	 aminocoumarin resistant parE;  clorobiocin;  aminocoumarin antibiotic;  novobiocin;  coumermycin A1;  antibiotic target alteration; 	model_description; model_param	"UPDATED model_description with Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
"
617	UPDATE	OXA-147	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
920	UPDATE	TEM-152	 penam;  antibiotic inactivation;  penem;  cephalosporin;  monobactam;  ampicillin;  TEM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4257	UPDATE	ADC-192	 antibiotic inactivation;  cephalosporin;  ADC beta-lactamases pending classification for carbapenemase activity; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2061	UPDATE	VIM-7	 penam;  antibiotic inactivation;  penem;  carbapenem;  cephalosporin;  cephamycin;  VIM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4256	UPDATE	ADC-191	 antibiotic inactivation;  cephalosporin;  ADC beta-lactamases pending classification for carbapenemase activity; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
922	UPDATE	AAC(6')-30/AAC(6')-Ib' fusion protein	 AAC(6');  antibiotic inactivation;  aminoglycoside antibiotic;  gentamicin A; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with gentamicin A
UPDATED category_aro_cvterm_id with 40942
UPDATED category_aro_accession with 3004015
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Gentamicin A is part of a complex of broad spectrum aminoglycoside antibiotics. Gentamicin inhibits protein synthesis, resulting in bacterial cell death.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
328	UPDATE	Salmonella enterica cmlA	 antibiotic efflux;  efflux pump complex or subunit conferring antibiotic resistance;  major facilitator superfamily (MFS) antibiotic efflux pump;  phenicol antibiotic;  chloramphenicol; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
923	UPDATE	VIM-25	 penam;  antibiotic inactivation;  penem;  carbapenem;  cephalosporin;  cephamycin;  VIM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3013	UPDATE	ADC-68	 carbapenem;  antibiotic inactivation;  ADC beta-lactamase with carbapenemase activity; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3014	UPDATE	IMP-55	 penam;  antibiotic inactivation;  penem;  carbapenem;  cephalosporin;  IMP beta-lactamase;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3015	UPDATE	IMP-56	 penam;  antibiotic inactivation;  penem;  carbapenem;  cephalosporin;  IMP beta-lactamase;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
519	UPDATE	VIM-26	 penam;  antibiotic inactivation;  penem;  carbapenem;  cephalosporin;  cephamycin;  VIM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
518	UPDATE	vanXY gene in vanN cluster	 glycopeptide antibiotic;  glycopeptide resistance gene cluster;  antibiotic target alteration;  vancomycin;  vanXY; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with vancomycin
UPDATED category_aro_cvterm_id with 35947
UPDATED category_aro_accession with 0000028
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.
UPDATED param_value with 125
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2149	UPDATE	Mycolicibacterium smegmatis 16S rRNA (rrsA) mutation conferring resistance to hygromycin B	 antibiotic target alteration;  hygromycin B;  aminoglycoside antibiotic;  16s rRNA with mutation conferring resistance to aminoglycoside antibiotics; 	model_description; model_param	"UPDATED model_description with Ribosomal RNA (rRNA) Gene Variant Models (RVM) are similar to Protein Variant Models (PVM), i.e. detect  sequences based on their similarity to a curated reference sequence and secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles, except RVMs are designed to detect AMR acquired via mutation of genes encoding ribosomal RNAs (rRNA). RVMs include a rRNA reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTN bit-score above the curated BLASTN cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTN bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
UPDATED param_description with The BLASTN bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
"
1009	UPDATE	IND-1	 carbapenem;  antibiotic inactivation;  IND beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1008	UPDATE	BEL-1	 penam;  monobactam;  cephalosporin;  antibiotic inactivation;  BEL beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1007	UPDATE	OKP-A-8	 penam;  antibiotic inactivation;  OKP beta-lactamase;  cephalosporin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
510	UPDATE	CTX-M-9	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1005	UPDATE	Escherichia coli soxR with mutation conferring antibiotic resistance	 antibiotic target alteration;  tetracycline antibiotic;  antibiotic efflux;  ATP-binding cassette (ABC) antibiotic efflux pump;  major facilitator superfamily (MFS) antibiotic efflux pump;  resistance-nodulation-cell division (RND) antibiotic efflux pump;  norfloxacin;  cephalosporin;  cefalotin;  ciprofloxacin;  disinfecting agents and antiseptics;  protein(s) and two-component regulatory system modulating antibiotic efflux;  rifampin;  ampicillin;  penam;  triclosan;  efflux pump complex or subunit conferring antibiotic resistance;  tigecycline;  glycylcycline;  fluoroquinolone antibiotic;  chloramphenicol;  phenicol antibiotic;  tetracycline;  rifamycin antibiotic; 	model_description; model_param	"UPDATED model_description with Protein Overexpression Models (POM) are similar to Protein Variant Models (PVM) in that they include a protein reference sequence, a curated BLASTP bitscore cut-off, and mapped resistance variants. Whereas PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, reporting only those with curated mutations conferring AMR, POMs are restricted to regulatory proteins and report both wild-type sequences and/or sequences with mutations leading to overexpression of efflux complexes. The former lead to efflux of antibiotics at basal levels, while the latter can confer clinical resistance. POMs include a protein reference sequence (often from wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Perfect RGI match is 100% identical to the wild-type reference protein sequence along its entire length, a Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value may or may not contain at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off may or may not contain at least one curated mutation from amongst the mapped resistance variants.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A frameshift mutation, caused by a nucleotide insertion or deletion that does not equal 3 bases, encoded as [wild-type][position]fs, for example S531fs. Termination can also be denoted as: Ter[position]fs.
UPDATED param_description with A subtype of the deletion mutation detection model parameter used when a set of deletion mutations are reported in a nucleotide sequence format, encoded as [-]nt[position]:[nucleotides], for example -nt25:T.
UPDATED param_description with A subtype of the deletion mutation detection model parameter used when a set of deletion mutations are reported in a peptide sequence format, encoded as [-][AAs][position range], for example -K527 or -QN517-518.
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
UPDATED param_description with A set of nucleotide or amino acid substitutions that are all required to confer resistance to an antibiotic drug or drug class, encoded as: [wild-type 1][position 1][mutation 1],[wild-type 2][position 2][mutation 2], etc. For example, D63Y,T142K.
"
512	UPDATE	CTX-M-82	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
515	UPDATE	mgtA	 antibiotic inactivation;  methymycin;  macrolide antibiotic;  mgt macrolide glycotransferase;  tylosin;  azithromycin;  erythromycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
514	UPDATE	LEN-10	 penam;  LEN beta-lactamase;  antibiotic inactivation;  penem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1001	UPDATE	Staphylococcus aureus mprF with mutation conferring resistance to daptomycin	 peptide antibiotic;  antibiotic target alteration;  daptomycin;  daptomycin resistant mprF; 	model_description; model_param	"UPDATED model_description with Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
"
1000	UPDATE	AAC(6')-Ib-Hangzhou	 AAC(6');  antibiotic inactivation;  aminoglycoside antibiotic; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4189	UPDATE	ADC-115	 antibiotic inactivation;  cephalosporin;  ADC beta-lactamases pending classification for carbapenemase activity; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1226	UPDATE	adeG	 antibiotic efflux;  resistance-nodulation-cell division (RND) antibiotic efflux pump;  efflux pump complex or subunit conferring antibiotic resistance;  tetracycline antibiotic;  fluoroquinolone antibiotic;  tetracycline; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
621	UPDATE	ErmF	 streptogramin A antibiotic;  antibiotic target alteration;  virginiamycin S2;  vernamycin C;  pristinamycin IC;  patricin B;  patricin A;  oleandomycin;  ostreogrycin B3;  macrolide antibiotic;  telithromycin;  tylosin;  lincosamide antibiotic;  dirithromycin;  clarithromycin;  clindamycin;  dalfopristin;  pristinamycin IB;  quinupristin;  pristinamycin IA;  Erm 23S ribosomal RNA methyltransferase;  virginiamycin M1;  madumycin II;  griseoviridin;  streptogramin B antibiotic;  lincomycin;  streptogramin antibiotic;  roxithromycin;  spiramycin;  azithromycin;  erythromycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1224	UPDATE	Erm(30)	 methymycin;  narbomycin;  Erm 23S ribosomal RNA methyltransferase;  pikromycin;  macrolide antibiotic;  antibiotic target alteration;  streptogramin antibiotic;  lincosamide antibiotic; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with methymycin
UPDATED category_aro_cvterm_id with 37631
UPDATED category_aro_accession with 3001232
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Produced by Streptomyces venezuelae ATCC 15439.
UPDATED category_aro_name with narbomycin
UPDATED category_aro_cvterm_id with 37625
UPDATED category_aro_accession with 3001226
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Produced by Streptomyces narbonensis.
UPDATED category_aro_name with pikromycin
UPDATED category_aro_cvterm_id with 37632
UPDATED category_aro_accession with 3001233
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Produced by Streptomyces venezuelae ATCC 15439.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
627	UPDATE	Escherichia coli rpoB mutants conferring resistance to rifampicin	 rifampin;  rifapentine;  rifabutin;  rifamycin-resistant beta-subunit of RNA polymerase (rpoB);  antibiotic target replacement;  antibiotic target alteration;  rifaximin;  rifamycin antibiotic; 	model_description; model_param	"UPDATED model_description with Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
UPDATED param_description with A frameshift mutation, caused by a nucleotide insertion or deletion that does not equal 3 bases, encoded as [wild-type][position]fs, for example S531fs. Termination can also be denoted as: Ter[position]fs.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
"
626	UPDATE	vanH gene in vanB cluster	 glycopeptide antibiotic;  glycopeptide resistance gene cluster;  vanH;  vancomycin;  antibiotic target alteration; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with vancomycin
UPDATED category_aro_cvterm_id with 35947
UPDATED category_aro_accession with 0000028
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.
UPDATED param_value with 200
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1221	UPDATE	OXA-231	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
624	UPDATE	Mycobacterium leprae rpoB mutations conferring resistance to rifampicin	 rifampin;  rifapentine;  rifabutin;  rifamycin-resistant beta-subunit of RNA polymerase (rpoB);  antibiotic target replacement;  antibiotic target alteration;  rifaximin;  rifamycin antibiotic; 	model_description; model_param	"UPDATED model_description with Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
"
4181	UPDATE	ADC-105	 antibiotic inactivation;  cephalosporin;  ADC beta-lactamases pending classification for carbapenemase activity; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4180	UPDATE	ADC-104	 antibiotic inactivation;  cephalosporin;  ADC beta-lactamases pending classification for carbapenemase activity; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4183	UPDATE	ADC-107	 antibiotic inactivation;  cephalosporin;  ADC beta-lactamases pending classification for carbapenemase activity; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4182	UPDATE	ADC-106	 antibiotic inactivation;  cephalosporin;  ADC beta-lactamases pending classification for carbapenemase activity; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4185	UPDATE	ADC-110	 antibiotic inactivation;  cephalosporin;  ADC beta-lactamases pending classification for carbapenemase activity; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4184	UPDATE	ADC-109	 antibiotic inactivation;  cephalosporin;  ADC beta-lactamases pending classification for carbapenemase activity; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4187	UPDATE	ADC-113	 antibiotic inactivation;  cephalosporin;  ADC beta-lactamases pending classification for carbapenemase activity; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4186	UPDATE	ADC-112	 antibiotic inactivation;  cephalosporin;  ADC beta-lactamases pending classification for carbapenemase activity; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5663	UPDATE	SPU-1	 carbapenem;  antibiotic inactivation;  SPU beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5662	UPDATE	SPS-1	 SPS beta-lactamase;  carbapenem;  antibiotic inactivation; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5661	UPDATE	SPR-1	 carbapenem;  SPR beta-lactamase;  antibiotic inactivation; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5660	UPDATE	SPN79-1	 carbapenem;  antibiotic inactivation;  SPN79 beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5666	UPDATE	STA-1	 STA beta-lactamase;  carbapenem;  antibiotic inactivation; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5665	UPDATE	SST-1	 antibiotic inactivation;  cephalosporin;  SST beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5664	UPDATE	SRT-3	 antibiotic inactivation;  cephalosporin;  SRT beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4347	UPDATE	ADC-91	 antibiotic inactivation;  cephalosporin;  ADC beta-lactamases pending classification for carbapenemase activity; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4346	UPDATE	ADC-90	 antibiotic inactivation;  cephalosporin;  ADC beta-lactamases pending classification for carbapenemase activity; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5669	UPDATE	TEM-99	 penam;  antibiotic inactivation;  penem;  cephalosporin;  monobactam;  ampicillin;  TEM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5668	UPDATE	TEM-98	 penam;  antibiotic inactivation;  penem;  cephalosporin;  monobactam;  ampicillin;  TEM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4343	UPDATE	ADC-87	 antibiotic inactivation;  cephalosporin;  ADC beta-lactamases pending classification for carbapenemase activity; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4342	UPDATE	ADC-86	 antibiotic inactivation;  cephalosporin;  ADC beta-lactamases pending classification for carbapenemase activity; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4341	UPDATE	ADC-85	 antibiotic inactivation;  cephalosporin;  ADC beta-lactamases pending classification for carbapenemase activity; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4340	UPDATE	ADC-84	 antibiotic inactivation;  cephalosporin;  ADC beta-lactamases pending classification for carbapenemase activity; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2882	UPDATE	tet(W/N/W)	 chlortetracycline;  tetracycline antibiotic;  antibiotic target protection;  minocycline;  tetracycline-resistant ribosomal protection protein;  tetracycline; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2880	UPDATE	QepA4	 efflux pump complex or subunit conferring antibiotic resistance;  fluoroquinolone antibiotic;  major facilitator superfamily (MFS) antibiotic efflux pump;  antibiotic efflux; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2881	UPDATE	tet(59)	 antibiotic efflux;  major facilitator superfamily (MFS) antibiotic efflux pump;  chlortetracycline;  oxytetracycline;  efflux pump complex or subunit conferring antibiotic resistance;  tetracycline antibiotic;  tetracycline; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2886	UPDATE	Haemophilus influenzae PBP3 conferring resistance to beta-lactam antibiotics	 penam;  cephamycin;  cefotaxime;  cefaclor;  cephalosporin;  Penicillin-binding protein mutations conferring resistance to beta-lactam antibiotics;  ampicillin;  cefditoren;  antibiotic target alteration;  ceftriaxone;  cefdinir; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
UPDATED category_aro_name with cefotaxime
UPDATED category_aro_cvterm_id with 36989
UPDATED category_aro_accession with 3000645
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Cefotaxime is a semisynthetic cephalosporin taken parenterally. It is resistant to most beta-lactamases and active against Gram-negative rods and cocci due to its aminothiazoyl and methoximino functional groups.
UPDATED category_aro_name with cefaclor
UPDATED category_aro_cvterm_id with 36988
UPDATED category_aro_accession with 3000644
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Cefaclor is a semisynthetic cephalosporin derived from cephalexin. It has broad-spectrum antibiotic activity.
UPDATED category_aro_name with ampicillin
UPDATED category_aro_cvterm_id with 36981
UPDATED category_aro_accession with 3000637
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.
UPDATED category_aro_name with cefditoren
UPDATED category_aro_cvterm_id with 36993
UPDATED category_aro_accession with 3000649
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Cefditoren is a semisynthetic cephalosporin active against staphylococci, streptococci, and and most enterobacteria. It is resistant to staphylococcal and most enterobacterial beta-lactamases, and is usually taken as the prodrug cefditoren pivoxil.
UPDATED category_aro_name with ceftriaxone
UPDATED category_aro_cvterm_id with 35979
UPDATED category_aro_accession with 0000062
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Ceftriaxone is a third-generation cephalosporin antibiotic. The presence of an aminothiazolyl sidechain increases ceftriazone's resistance to beta-lactamases. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria.
UPDATED category_aro_name with cefdinir
UPDATED category_aro_cvterm_id with 36994
UPDATED category_aro_accession with 3000650
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Cefdinir is similar to cefixime with a modified side-chain at its 7-amino position. It also shares similar activity with cefixime but is more active against staphylococci. It has also be shown to enhance phagocytosis.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
"
2884	UPDATE	RSA-1	 carbapenem;  antibiotic inactivation;  cephalosporin;  RSA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2885	UPDATE	RSA-2	 carbapenem;  antibiotic inactivation;  cephalosporin;  RSA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1072	UPDATE	OXA-37	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2888	UPDATE	HERA-1	 penam;  HERA beta-lactamase;  antibiotic inactivation; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2889	UPDATE	TRU-1	 penam;  antibiotic inactivation;  cephalosporin;  TRU beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2	UPDATE	CblA-1	 antibiotic inactivation;  CblA beta-lactamase;  cephaloridine;  cephalosporin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3878	UPDATE	PDC-69	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3879	UPDATE	APH(3')-XV	 antibiotic inactivation;  kanamycin A;  APH(3');  amikacin;  aminoglycoside antibiotic;  G418;  neomycin; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with kanamycin A
UPDATED category_aro_cvterm_id with 35966
UPDATED category_aro_accession with 0000049
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.
UPDATED category_aro_name with amikacin
UPDATED category_aro_cvterm_id with 35932
UPDATED category_aro_accession with 0000013
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3870	UPDATE	PDC-61	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3871	UPDATE	PDC-45	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3872	UPDATE	PDC-49	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3873	UPDATE	PDC-50	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3874	UPDATE	PDC-48	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3875	UPDATE	PAC-1	 antibiotic inactivation;  cephalosporin;  PAC beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3876	UPDATE	PDC-53	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3877	UPDATE	PDC-72	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4395	UPDATE	BlaB-33	 carbapenem;  penam;  antibiotic inactivation;  BlaB beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1286	UPDATE	SHV-34	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  SHV beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1714	UPDATE	ErmW	 Erm 23S ribosomal RNA methyltransferase;  josamycin;  macrolide antibiotic;  antibiotic target alteration;  streptogramin antibiotic;  erythromycin;  lincosamide antibiotic; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with erythromycin
UPDATED category_aro_cvterm_id with 35925
UPDATED category_aro_accession with 0000006
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure/function processes critical for life or replication are inhibited.
UPDATED category_aro_name with josamycin
UPDATED category_aro_cvterm_id with 37620
UPDATED category_aro_accession with 3001221
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with A macrolide antibiotic from Streptomyces narbonensis subsp. josamyceticus. The drug has antimicrobial activity against a wide spectrum of pathogens.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4677	UPDATE	IMI-6	 carbapenem;  antibiotic inactivation;  IMI beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1043	UPDATE	SHV-76	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  SHV beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
11	UPDATE	Erm(34)	 streptogramin A antibiotic;  antibiotic target alteration;  virginiamycin S2;  vernamycin C;  pristinamycin IC;  patricin B;  patricin A;  oleandomycin;  ostreogrycin B3;  macrolide antibiotic;  telithromycin;  tylosin;  lincosamide antibiotic;  dirithromycin;  clarithromycin;  clindamycin;  dalfopristin;  pristinamycin IB;  quinupristin;  pristinamycin IA;  Erm 23S ribosomal RNA methyltransferase;  virginiamycin M1;  madumycin II;  griseoviridin;  streptogramin B antibiotic;  lincomycin;  streptogramin antibiotic;  roxithromycin;  spiramycin;  azithromycin;  erythromycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
10	UPDATE	CARB-5	 penam;  antibiotic inactivation;  CARB beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
13	UPDATE	LRA-12	 penam;  antibiotic inactivation;  subclass B3 LRA beta-lactamase;  cephalosporin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
12	UPDATE	TEM-126	 penam;  antibiotic inactivation;  penem;  cephalosporin;  monobactam;  ampicillin;  TEM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
15	UPDATE	TEM-59	 penam;  antibiotic inactivation;  penem;  cephalosporin;  monobactam;  ampicillin;  TEM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
14	UPDATE	TEM-72	 penam;  antibiotic inactivation;  penem;  cephalosporin;  monobactam;  ampicillin;  TEM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5719	UPDATE	VIM-70	 penam;  antibiotic inactivation;  penem;  carbapenem;  cephalosporin;  cephamycin;  VIM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5718	UPDATE	VIM-69	 penam;  antibiotic inactivation;  penem;  carbapenem;  cephalosporin;  cephamycin;  VIM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5717	UPDATE	VIM-68	 penam;  antibiotic inactivation;  penem;  carbapenem;  cephalosporin;  cephamycin;  VIM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5716	UPDATE	VIM-67	 penam;  antibiotic inactivation;  penem;  carbapenem;  cephalosporin;  cephamycin;  VIM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5715	UPDATE	VIM-66	 penam;  antibiotic inactivation;  penem;  carbapenem;  cephalosporin;  cephamycin;  VIM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5714	UPDATE	VIM-65	 penam;  antibiotic inactivation;  penem;  carbapenem;  cephalosporin;  cephamycin;  VIM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5713	UPDATE	VIM-64	 penam;  antibiotic inactivation;  penem;  carbapenem;  cephalosporin;  cephamycin;  VIM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5712	UPDATE	VIM-63	 penam;  antibiotic inactivation;  penem;  carbapenem;  cephalosporin;  cephamycin;  VIM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5711	UPDATE	VIM-62	 penam;  antibiotic inactivation;  penem;  carbapenem;  cephalosporin;  cephamycin;  VIM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5710	UPDATE	VIM-61	 penam;  antibiotic inactivation;  penem;  carbapenem;  cephalosporin;  cephamycin;  VIM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1924	UPDATE	vanM	 glycopeptide resistance gene cluster;  Van ligase;  teicoplanin;  glycopeptide antibiotic;  antibiotic target alteration;  vancomycin; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with vancomycin
UPDATED category_aro_cvterm_id with 35947
UPDATED category_aro_accession with 0000028
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.
UPDATED category_aro_name with teicoplanin
UPDATED category_aro_cvterm_id with 35948
UPDATED category_aro_accession with 0000029
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Teicoplanin is a glycopeptide antibiotic used in the prophylaxis and treatment of serious infections caused by Gram-positive bacteria. Teicoplanin has a unique acyl-aliphatic chain, and binds to cell wall precursors to inhibit transglycosylation  and transpeptidation.
UPDATED param_value with 350
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3904	UPDATE	CMY-165	 antibiotic inactivation;  CMY beta-lactamase;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3905	UPDATE	CMY-166	 antibiotic inactivation;  CMY beta-lactamase;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3906	UPDATE	CMY-149	 antibiotic inactivation;  CMY beta-lactamase;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3907	UPDATE	CMY-139	 antibiotic inactivation;  CMY beta-lactamase;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3900	UPDATE	CMY-162	 antibiotic inactivation;  CMY beta-lactamase;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3901	UPDATE	CMY-140	 antibiotic inactivation;  CMY beta-lactamase;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3902	UPDATE	CMY-164	 antibiotic inactivation;  CMY beta-lactamase;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3903	UPDATE	CMY-161	 antibiotic inactivation;  CMY beta-lactamase;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1927	UPDATE	SHV-29	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  SHV beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3908	UPDATE	CMY-148	 antibiotic inactivation;  CMY beta-lactamase;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3909	UPDATE	CMY-163	 antibiotic inactivation;  CMY beta-lactamase;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4761	UPDATE	MAL-2	 carbapenem;  antibiotic inactivation;  MAL beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4760	UPDATE	MAL-1	 carbapenem;  antibiotic inactivation;  MAL beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4763	UPDATE	MIR-18	 antibiotic inactivation;  monobactam;  cephalosporin;  MIR beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4762	UPDATE	MBL1b	 carbapenem;  antibiotic inactivation;  MBL beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4765	UPDATE	MIR-20	 antibiotic inactivation;  monobactam;  cephalosporin;  MIR beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4764	UPDATE	MIR-19	 antibiotic inactivation;  monobactam;  cephalosporin;  MIR beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4767	UPDATE	MIR-22	 antibiotic inactivation;  monobactam;  cephalosporin;  MIR beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4766	UPDATE	MIR-21	 antibiotic inactivation;  monobactam;  cephalosporin;  MIR beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4769	UPDATE	MOC-1	 carbapenem;  antibiotic inactivation;  MOC beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4768	UPDATE	MIR-7	 antibiotic inactivation;  monobactam;  cephalosporin;  MIR beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4167	UPDATE	ACT-77	 antibiotic inactivation;  carbapenem;  penam;  ACT beta-lactamase;  cephalosporin;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4166	UPDATE	ACT-76	 antibiotic inactivation;  carbapenem;  penam;  ACT beta-lactamase;  cephalosporin;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4165	UPDATE	ACT-75	 antibiotic inactivation;  carbapenem;  penam;  ACT beta-lactamase;  cephalosporin;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4164	UPDATE	ACT-74	 antibiotic inactivation;  carbapenem;  penam;  ACT beta-lactamase;  cephalosporin;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4163	UPDATE	ACT-73	 antibiotic inactivation;  carbapenem;  penam;  ACT beta-lactamase;  cephalosporin;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4162	UPDATE	ACT-72	 antibiotic inactivation;  carbapenem;  penam;  ACT beta-lactamase;  cephalosporin;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4161	UPDATE	ACT-70	 antibiotic inactivation;  carbapenem;  penam;  ACT beta-lactamase;  cephalosporin;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4160	UPDATE	ACT-69	 antibiotic inactivation;  carbapenem;  penam;  ACT beta-lactamase;  cephalosporin;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
599	UPDATE	OKP-A-3	 penam;  antibiotic inactivation;  OKP beta-lactamase;  cephalosporin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3604	UPDATE	GOB-3	 carbapenem;  penam;  GOB beta-lactamase;  antibiotic inactivation;  cephalosporin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4169	UPDATE	ACT-79	 antibiotic inactivation;  carbapenem;  penam;  ACT beta-lactamase;  cephalosporin;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4168	UPDATE	ACT-78	 antibiotic inactivation;  carbapenem;  penam;  ACT beta-lactamase;  cephalosporin;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1471	UPDATE	adeI	 antibiotic efflux;  imipenem;  rifampin;  resistance-nodulation-cell division (RND) antibiotic efflux pump;  trimethoprim;  rifamycin antibiotic;  penem;  macrolide antibiotic;  carbapenem;  efflux pump complex or subunit conferring antibiotic resistance;  cephalosporin;  diaminopyrimidine antibiotic;  ticarcillin;  tetracycline antibiotic;  fluoroquinolone antibiotic;  lincosamide antibiotic;  phenicol antibiotic;  tetracycline;  chloramphenicol; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1073	UPDATE	OKP-B-19	 penam;  antibiotic inactivation;  OKP beta-lactamase;  cephalosporin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
201	UPDATE	OCH-3	 penam;  antibiotic inactivation;  penem;  cephalosporin;  cephamycin;  monobactam;  OCH beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
200	UPDATE	LEN-14	 penam;  LEN beta-lactamase;  antibiotic inactivation;  penem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
203	UPDATE	OXY-2-8	 penam;  OXY beta-lactamase;  cephalosporin;  antibiotic inactivation;  monobactam; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
202	UPDATE	SHV-101	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  SHV beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
205	UPDATE	APH(4)-Ia	 antibiotic inactivation;  hygromycin B;  aminoglycoside antibiotic;  APH(4);  plazomicin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
204	UPDATE	VIM-43	 penam;  antibiotic inactivation;  penem;  carbapenem;  cephalosporin;  cephamycin;  VIM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
207	UPDATE	GES-12	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  GES beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
206	UPDATE	FomA	 fosfomycin;  phosphonic acid antibiotic;  antibiotic inactivation;  Fom phosphotransferase family; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_name with phosphonic acid antibiotic
UPDATED category_aro_cvterm_id with 45731
UPDATED category_aro_accession with 3007149
UPDATED category_aro_class_name with Drug Class
UPDATED category_aro_description with A group of antibiotics derived from phosphonic acids.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
209	UPDATE	AAC(3)-Ib/AAC(6')-Ib''	 antibiotic inactivation;  AAC(3);  AAC(6');  kanamycin A;  gentamicin C;  aminoglycoside antibiotic;  tobramycin; 	model_description; model_param; ARO_name	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED ARO_name with AAC(3)-Ib/AAC(6')-Ib'' fusion protein
"
208	UPDATE	CMY-105	 antibiotic inactivation;  CMY beta-lactamase;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2745	UPDATE	AcrAB-TolC	 penam;  antibiotic efflux;  triclosan;  rifampin;  resistance-nodulation-cell division (RND) antibiotic efflux pump;  efflux pump complex or subunit conferring antibiotic resistance;  disinfecting agents and antiseptics;  tetracycline antibiotic;  cephalosporin;  cefalotin;  tigecycline;  glycylcycline;  ampicillin;  fluoroquinolone antibiotic;  rifamycin antibiotic;  phenicol antibiotic;  tetracycline;  chloramphenicol; 	model_description; model_param	"UPDATED model_description with Efflux Pump System Meta-Models (EPS) are dedicated to efflux complexes and their regulators, such as AcrAB-TolC. Using the efflux pump components parameter, this model type simply includes a list of detection models for each component of the complex. This model type is still under development and not currently supported by the Resistance Gene Identifier (RGI) software.
UPDATED param_description with Association of proteins within efflux protein complexes or regulatory networks are encoded by the efflux pump components parameter: model_id,model_id,model_id, etc.
"
830	UPDATE	SHV-157	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  SHV beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
642	UPDATE	aadA25	 antibiotic inactivation;  aminoglycoside antibiotic;  ANT(3'');  streptomycin;  spectinomycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1573	UPDATE	SHV-110	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  SHV beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
831	UPDATE	OKP-B-13	 penam;  antibiotic inactivation;  OKP beta-lactamase;  cephalosporin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1827	UPDATE	SHV-5	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  SHV beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1572	UPDATE	OXA-205	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
836	UPDATE	TEM-68	 penam;  antibiotic inactivation;  penem;  cephalosporin;  monobactam;  ampicillin;  TEM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2250	UPDATE	fusC	 antibiotic target protection;  fusidic acid;  fusidane antibiotic;  Target protecting FusB-type protein conferring resistance to Fusidic acid; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_name with fusidane antibiotic
UPDATED category_aro_cvterm_id with 45735
UPDATED category_aro_accession with 3007153
UPDATED category_aro_class_name with Drug Class
UPDATED category_aro_description with A group of antibiotics possessing steroid rings or steroid-like structures.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1571	UPDATE	vanS gene in vanE cluster	 glycopeptide antibiotic;  vanS;  antibiotic target alteration;  vancomycin;  glycopeptide resistance gene cluster; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with vancomycin
UPDATED category_aro_cvterm_id with 35947
UPDATED category_aro_accession with 0000028
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
837	UPDATE	vatH	 dalfopristin;  antibiotic inactivation;  streptogramin vat acetyltransferase;  virginiamycin M1;  madumycin II;  griseoviridin;  streptogramin A antibiotic;  streptogramin antibiotic; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1570	UPDATE	OprA	 antibiotic efflux;  tobramycin;  resistance-nodulation-cell division (RND) antibiotic efflux pump;  ofloxacin;  norfloxacin;  meropenem;  macrolide antibiotic;  carbapenem;  efflux pump complex or subunit conferring antibiotic resistance;  arbekacin;  ciprofloxacin;  tetracycline antibiotic;  gentamicin C;  amikacin;  aminoglycoside antibiotic;  fluoroquinolone antibiotic;  tetracycline;  erythromycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
834	UPDATE	FosA3	 antibiotic inactivation;  fosfomycin thiol transferase;  phosphonic acid antibiotic; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
DELETED 35944
UPDATED category_aro_name with phosphonic acid antibiotic
UPDATED category_aro_cvterm_id with 45731
UPDATED category_aro_accession with 3007149
UPDATED category_aro_class_name with Drug Class
UPDATED category_aro_description with A group of antibiotics derived from phosphonic acids.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
998	UPDATE	SHV-134	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  SHV beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2231	UPDATE	CPS-1	 carbapenem;  antibiotic inactivation;  CPS beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2230	UPDATE	PEDO-3	 carbapenem;  antibiotic inactivation;  subclass B1 PEDO beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2233	UPDATE	MSI-1	 carbapenem;  antibiotic inactivation;  MSI beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2232	UPDATE	ESP-1	 carbapenem;  antibiotic inactivation;  ESP beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2235	UPDATE	SPG-1	 carbapenem;  SPG beta-lactamase;  antibiotic inactivation; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2234	UPDATE	MSI-OXA	 MSI-OXA family beta-lactamase;  carbapenem;  antibiotic inactivation; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1576	UPDATE	OXA-17	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3575	UPDATE	CME-1	 penam;  antibiotic inactivation;  CME beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1575	UPDATE	OXA-91	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3574	UPDATE	CKO-1	 CKO beta-lactamase;  penam;  antibiotic inactivation; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1574	UPDATE	Mycobacterium tuberculosis inhA mutations conferring resistance to isoniazid	 antibiotic target alteration;  isoniazid-like antibiotic;  isoniazid resistant inhA; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
DELETED 36659
UPDATED category_aro_name with isoniazid-like antibiotic
UPDATED category_aro_cvterm_id with 45734
UPDATED category_aro_accession with 3007152
UPDATED category_aro_class_name with Drug Class
UPDATED category_aro_description with A group of antibiotics containing isoniazid and its derivatives.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
"
1711	UPDATE	AQU-1	 antibiotic inactivation;  AQU beta-lactamase;  cephalosporin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3577	UPDATE	CMY-132	 antibiotic inactivation;  CMY beta-lactamase;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1631	UPDATE	CTX-M-71	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3576	UPDATE	CMH-1	 antibiotic inactivation;  CMH beta-lactamase;  cephalosporin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
229	UPDATE	vanTm gene in vanL cluster	 glycopeptide antibiotic;  glycopeptide resistance gene cluster;  antibiotic target alteration;  vancomycin;  vanT; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with vancomycin
UPDATED category_aro_cvterm_id with 35947
UPDATED category_aro_accession with 0000028
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.
UPDATED param_value with 175
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3498	UPDATE	OXA-414	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3499	UPDATE	OXA-416	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3496	UPDATE	OXA-412	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3497	UPDATE	OXA-413	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3494	UPDATE	OXA-409	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3495	UPDATE	OXA-411	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3492	UPDATE	OXA-407	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3493	UPDATE	OXA-408	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3490	UPDATE	OXA-405	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3491	UPDATE	OXA-406	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4570	UPDATE	CTX-M-241	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4571	UPDATE	CTX-M-242	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4572	UPDATE	CTX-M-244	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4573	UPDATE	CTX-M-73	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3658	UPDATE	NDM-16	 antibiotic inactivation;  penam;  carbapenem;  cephalosporin;  cephamycin;  NDM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3659	UPDATE	NDM-18	 antibiotic inactivation;  penam;  carbapenem;  cephalosporin;  cephamycin;  NDM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4576	UPDATE	DHA-23	 antibiotic inactivation;  cephalosporin;  cephamycin;  DHA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4607	UPDATE	FOX-17	 antibiotic inactivation;  cephamycin;  cephalosporin;  FOX beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4578	UPDATE	DHA-25	 antibiotic inactivation;  cephalosporin;  cephamycin;  DHA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4579	UPDATE	DHA-26	 antibiotic inactivation;  cephalosporin;  cephamycin;  DHA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3656	UPDATE	Burkholderia dolosa gyrA conferring resistance to fluoroquinolones	 antibiotic target alteration;  fluoroquinolone antibiotic;  fluoroquinolone resistant gyrA;  ciprofloxacin; 	model_description; model_param	"UPDATED model_description with Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
"
3657	UPDATE	NDM-15	 antibiotic inactivation;  penam;  carbapenem;  cephalosporin;  cephamycin;  NDM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2099	UPDATE	Mycolicibacterium smegmatis 16S rRNA (rrsB) mutation conferring resistance to kanamycin A	 kanamycin A;  antibiotic target alteration;  aminoglycoside antibiotic;  16s rRNA with mutation conferring resistance to aminoglycoside antibiotics; 	model_description; model_param	"UPDATED model_description with Ribosomal RNA (rRNA) Gene Variant Models (RVM) are similar to Protein Variant Models (PVM), i.e. detect  sequences based on their similarity to a curated reference sequence and secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles, except RVMs are designed to detect AMR acquired via mutation of genes encoding ribosomal RNAs (rRNA). RVMs include a rRNA reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTN bit-score above the curated BLASTN cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTN bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
UPDATED param_description with The BLASTN bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
"
3651	UPDATE	Mycobacterium tuberculosis 16S rRNA mutation conferring resistance to capreomycin	 antibiotic target alteration;  capreomycin;  aminoglycoside antibiotic;  16s rRNA with mutation conferring resistance to aminoglycoside antibiotics; 	model_description; model_param	"UPDATED model_description with Ribosomal RNA (rRNA) Gene Variant Models (RVM) are similar to Protein Variant Models (PVM), i.e. detect  sequences based on their similarity to a curated reference sequence and secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles, except RVMs are designed to detect AMR acquired via mutation of genes encoding ribosomal RNAs (rRNA). RVMs include a rRNA reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTN bit-score above the curated BLASTN cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTN bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
UPDATED param_description with The BLASTN bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
"
3652	UPDATE	CMY-136	 antibiotic inactivation;  cefotaxime;  cephalosporin;  cephamycin;  cefuroxime;  CMY beta-lactamase;  ceftolozane; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3653	UPDATE	SCO-1	 penam;  cefalotin;  antibiotic inactivation;  penicillin;  penem;  piperacillin-tazobactam;  cephalosporin;  cefotaxime;  ceftazidime;  cefepime;  SCO beta-lactamase;  ticarcillin;  ticarcillin-clavulanic acid;  amoxicillin;  cefuroxime;  clavulanic acid;  piperacillin;  tazobactam;  amoxicillin-clavulanic acid; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2525	UPDATE	AAC(6')-34	 AAC(6');  kanamycin A;  antibiotic inactivation;  aminoglycoside antibiotic; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with kanamycin A
UPDATED category_aro_cvterm_id with 35966
UPDATED category_aro_accession with 0000049
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2524	UPDATE	AAC(2')-IIb	 antibiotic inactivation;  aminoglycoside antibiotic;  AAC(2');  kasugamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2527	UPDATE	mphI	 antibiotic inactivation;  macrolide phosphotransferase (MPH);  macrolide antibiotic;  telithromycin;  tylosin;  erythromycin; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with telithromycin
UPDATED category_aro_cvterm_id with 35974
UPDATED category_aro_accession with 0000057
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Telithromycin is a semi-synthetic derivative of erythromycin. It is a 14-membered macrolide and is the first ketolide antibiotic to be used in clinics. Telithromycin binds the 50S subunit of the bacterial ribosome to inhibit protein synthesis.
UPDATED category_aro_name with tylosin
UPDATED category_aro_cvterm_id with 36284
UPDATED category_aro_accession with 3000145
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Tylosin is a 16-membered macrolide, naturally produced by Streptomyces fradiae. It interacts with the bacterial ribosome 50S subunit to inhibit protein synthesis.
UPDATED category_aro_name with erythromycin
UPDATED category_aro_cvterm_id with 35925
UPDATED category_aro_accession with 0000006
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure/function processes critical for life or replication are inhibited.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2526	UPDATE	vgbC	 virginiamycin S2;  pristinamycin IB;  quinupristin;  pristinamycin IC;  patricin B;  patricin A;  ostreogrycin B3;  vernamycin C;  streptogramin B antibiotic;  pristinamycin IA;  antibiotic inactivation;  streptogramin antibiotic;  streptogramin vgb lyase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2521	UPDATE	BahA	 Bah amidohydrolase;  peptide antibiotic;  bacitracin;  antibiotic inactivation; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with bacitracin
UPDATED category_aro_cvterm_id with 35959
UPDATED category_aro_accession with 0000041
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Bacitracin is a mixture of related cyclic polypeptides produced by organisms of the licheniformis group of Bacillus subtilis var Tracy. Bacitracin interferes with the dephosphorylation of the C55-isoprenyl pyrophosphate, a molecule which carries the building blocks of the peptidoglycan bacterial cell wall outside of the inner membrane.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2520	UPDATE	CatU	 antibiotic inactivation;  thiamphenicol;  chloramphenicol acetyltransferase (CAT);  azidamfenicol;  phenicol antibiotic;  chloramphenicol; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2523	UPDATE	VatI	 dalfopristin;  antibiotic inactivation;  streptogramin vat acetyltransferase;  virginiamycin M1;  madumycin II;  griseoviridin;  streptogramin A antibiotic;  streptogramin antibiotic; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2522	UPDATE	TaeA	 pleuromutilin;  ATP-binding cassette (ABC) antibiotic efflux pump;  antibiotic efflux;  pleuromutilin antibiotic;  efflux pump complex or subunit conferring antibiotic resistance; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4602	UPDATE	FOX-12	 antibiotic inactivation;  cephamycin;  cephalosporin;  FOX beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2529	UPDATE	cpaA	 antibiotic inactivation;  capreomycin;  aminoglycoside antibiotic;  cpa acetyltransferase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2528	UPDATE	rphB	 antibiotic inactivation;  rifampin;  rifapentine;  rifampin phosphotransferase;  rifabutin;  rifaximin;  rifamycin antibiotic; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4603	UPDATE	FOX-13	 antibiotic inactivation;  cephamycin;  cephalosporin;  FOX beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4600	UPDATE	EVM-1	 carbapenem;  antibiotic inactivation;  EVM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4601	UPDATE	FIA-1	 carbapenem;  antibiotic inactivation;  FIA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
598	UPDATE	dfrA16	 trimethoprim;  diaminopyrimidine antibiotic;  trimethoprim resistant dihydrofolate reductase dfr;  antibiotic target replacement; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5065	UPDATE	OXA-756	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5064	UPDATE	OXA-755	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5067	UPDATE	OXA-758	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5066	UPDATE	OXA-757	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5061	UPDATE	OXA-752	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5060	UPDATE	OXA-751	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5063	UPDATE	OXA-754	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5062	UPDATE	OXA-753	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4880	UPDATE	OXA-551	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2704	UPDATE	MexEF-OprN with MexT mutation conferring resistance to chloramphenicol, ciprofloxacin, and trimethoprim	 antibiotic efflux;  resistance-nodulation-cell division (RND) antibiotic efflux pump;  trimethoprim;  efflux pump complex or subunit conferring antibiotic resistance;  diaminopyrimidine antibiotic;  ciprofloxacin;  fluoroquinolone antibiotic;  phenicol antibiotic;  chloramphenicol; 	model_description; model_param	"UPDATED model_description with Efflux Pump System Meta-Models (EPS) are dedicated to efflux complexes and their regulators, such as AcrAB-TolC. Using the efflux pump components parameter, this model type simply includes a list of detection models for each component of the complex. This model type is still under development and not currently supported by the Resistance Gene Identifier (RGI) software.
UPDATED param_description with Association of proteins within efflux protein complexes or regulatory networks are encoded by the efflux pump components parameter: model_id,model_id,model_id, etc.
"
4882	UPDATE	OXA-553	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2706	UPDATE	MvaT	 antibiotic efflux;  resistance-nodulation-cell division (RND) antibiotic efflux pump;  protein(s) and two-component regulatory system modulating antibiotic efflux;  norfloxacin;  trimethoprim;  efflux pump complex or subunit conferring antibiotic resistance;  diaminopyrimidine antibiotic;  fluoroquinolone antibiotic;  phenicol antibiotic;  chloramphenicol; 	model_description; model_param	"UPDATED model_description with Protein Knockout Models (PKM) reflect resistance by the absence of a gene product, most often deletion of a gene involved in antibiotic import, such as Vibrio cholerae OmpT. Like Protein Homolog Models (PHMs), PKMs include a reference sequence and a bitscore cut-off for detection using BLASTP but instead are designed to only report lack of detection under Perfect or Strict criteria. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff. This model type is still under development and not currently supported by the Resistance Gene Identifier (RGI) software.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5069	UPDATE	OXA-760	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4885	UPDATE	OXA-556	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4886	UPDATE	OXA-557	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4887	UPDATE	OXA-558	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1070	UPDATE	sul1	 sulfadiazine;  sulfadoxine;  sulfacetamide;  sulfadimidine;  mafenide;  sulfamethoxazole;  sulfisoxazole;  sulfonamide resistant sul;  antibiotic target replacement;  sulfamethizole;  sulfasalazine;  sulfonamide antibiotic; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4090	UPDATE	KPC-26	 antibiotic inactivation;  penam;  carbapenem;  cephalosporin;  monobactam;  KPC beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4719	UPDATE	KPC-21	 antibiotic inactivation;  penam;  carbapenem;  cephalosporin;  monobactam;  KPC beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4408	UPDATE	CAR-1	 carbapenem;  antibiotic inactivation;  CAR beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4409	UPDATE	CARB-11	 penam;  antibiotic inactivation;  CARB beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4404	UPDATE	BlaB-8	 carbapenem;  penam;  antibiotic inactivation;  BlaB beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4405	UPDATE	BlaB-9	 carbapenem;  penam;  antibiotic inactivation;  BlaB beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4406	UPDATE	BSU-1	 carbapenem;  antibiotic inactivation;  BSU beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4407	UPDATE	BUT-2	 BUT beta-lactamase;  antibiotic inactivation;  cephalosporin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4400	UPDATE	BlaB-39	 carbapenem;  penam;  antibiotic inactivation;  BlaB beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4401	UPDATE	BlaB-5	 carbapenem;  penam;  antibiotic inactivation;  BlaB beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4402	UPDATE	BlaB-6	 carbapenem;  penam;  antibiotic inactivation;  BlaB beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4403	UPDATE	BlaB-7	 carbapenem;  penam;  antibiotic inactivation;  BlaB beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
928	UPDATE	carA	 carbomycin;  Miscellaneous ABC-F subfamily ATP-binding cassette ribosomal protection proteins;  antibiotic target protection;  macrolide antibiotic; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2146	UPDATE	Escherichia coli 16S rRNA (rrnB) mutation conferring resistance to streptomycin	 antibiotic target alteration;  streptomycin;  aminoglycoside antibiotic;  16s rRNA with mutation conferring resistance to aminoglycoside antibiotics; 	model_description; model_param	"UPDATED model_description with Ribosomal RNA (rRNA) Gene Variant Models (RVM) are similar to Protein Variant Models (PVM), i.e. detect  sequences based on their similarity to a curated reference sequence and secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles, except RVMs are designed to detect AMR acquired via mutation of genes encoding ribosomal RNAs (rRNA). RVMs include a rRNA reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTN bit-score above the curated BLASTN cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTN bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
UPDATED param_description with The BLASTN bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
"
2145	UPDATE	Escherichia coli 16S rRNA (rrsB) mutation conferring resistance to tetracycline	 tetracycline antibiotic;  antibiotic target alteration;  16S rRNA with mutation conferring resistance to tetracycline derivatives;  tetracycline; 	model_description; model_param	"UPDATED model_description with Ribosomal RNA (rRNA) Gene Variant Models (RVM) are similar to Protein Variant Models (PVM), i.e. detect  sequences based on their similarity to a curated reference sequence and secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles, except RVMs are designed to detect AMR acquired via mutation of genes encoding ribosomal RNAs (rRNA). RVMs include a rRNA reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTN bit-score above the curated BLASTN cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTN bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
UPDATED param_description with The BLASTN bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
"
2144	UPDATE	Mycobacterium tuberculosis variant bovis embB with mutation conferring resistance to ethambutol	 antibiotic target alteration;  polyamine antibiotic;  ethambutol;  ethambutol resistant embB; 	model_description; model_param	"UPDATED model_description with Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
"
4978	UPDATE	OXA-658	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4979	UPDATE	OXA-659	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2141	UPDATE	Mycolicibacterium smegmatis 16S rRNA (rrsB) mutation conferring resistance to neomycin	 antibiotic target alteration;  aminoglycoside antibiotic;  16s rRNA with mutation conferring resistance to aminoglycoside antibiotics;  neomycin; 	model_description; model_param	"UPDATED model_description with Ribosomal RNA (rRNA) Gene Variant Models (RVM) are similar to Protein Variant Models (PVM), i.e. detect  sequences based on their similarity to a curated reference sequence and secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles, except RVMs are designed to detect AMR acquired via mutation of genes encoding ribosomal RNAs (rRNA). RVMs include a rRNA reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTN bit-score above the curated BLASTN cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTN bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
UPDATED param_description with The BLASTN bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
"
2140	UPDATE	Escherichia coli 16S rRNA (rrsB) mutation conferring resistance to streptomycin	 antibiotic target alteration;  streptomycin;  aminoglycoside antibiotic;  16s rRNA with mutation conferring resistance to aminoglycoside antibiotics; 	model_description; model_param	"UPDATED model_description with Ribosomal RNA (rRNA) Gene Variant Models (RVM) are similar to Protein Variant Models (PVM), i.e. detect  sequences based on their similarity to a curated reference sequence and secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles, except RVMs are designed to detect AMR acquired via mutation of genes encoding ribosomal RNAs (rRNA). RVMs include a rRNA reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTN bit-score above the curated BLASTN cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTN bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
UPDATED param_description with The BLASTN bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
"
4974	UPDATE	OXA-654	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
921	UPDATE	OKP-A-11	 penam;  antibiotic inactivation;  OKP beta-lactamase;  cephalosporin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4976	UPDATE	OXA-656	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4977	UPDATE	OXA-657	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4970	UPDATE	OXA-645	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4971	UPDATE	OXA-650	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4972	UPDATE	OXA-651	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4229	UPDATE	ADC-160	 antibiotic inactivation;  cephalosporin;  ADC beta-lactamases pending classification for carbapenemase activity; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5393	UPDATE	PDC-254	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5392	UPDATE	PDC-253	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5391	UPDATE	PDC-252	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5390	UPDATE	PDC-251	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5397	UPDATE	PDC-260	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5396	UPDATE	PDC-26	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5395	UPDATE	PDC-259	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5394	UPDATE	PDC-256	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2411	UPDATE	Shigella flexneri gyrA conferring resistance to fluoroquinolones	 antibiotic target alteration;  norfloxacin;  nalidixic acid;  fluoroquinolone antibiotic;  fluoroquinolone resistant gyrA; 	model_description; model_param	"UPDATED model_description with Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
"
5399	UPDATE	PDC-262	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5398	UPDATE	PDC-261	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1920	UPDATE	vanS gene in vanF cluster	 glycopeptide antibiotic;  vanS;  antibiotic target alteration;  vancomycin;  glycopeptide resistance gene cluster; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with vancomycin
UPDATED category_aro_cvterm_id with 35947
UPDATED category_aro_accession with 0000028
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1921	UPDATE	EreB	 antibiotic inactivation;  macrolide esterase;  macrolide antibiotic;  roxithromycin;  clarithromycin;  azithromycin;  erythromycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1922	UPDATE	marA	 penem;  tetracycline antibiotic;  antibiotic efflux;  rifampin;  resistance-nodulation-cell division (RND) antibiotic efflux pump;  reduced permeability to antibiotic;  carbapenem;  cephalosporin;  cefalotin;  disinfecting agents and antiseptics;  protein(s) and two-component regulatory system modulating antibiotic efflux;  ampicillin;  penam;  triclosan;  efflux pump complex or subunit conferring antibiotic resistance;  cephamycin;  tigecycline;  glycylcycline;  General Bacterial Porin with reduced permeability to beta-lactams;  monobactam;  fluoroquinolone antibiotic;  chloramphenicol;  phenicol antibiotic;  tetracycline;  rifamycin antibiotic; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1923	UPDATE	APH(3'')-Ia	 antibiotic inactivation;  APH(3'');  streptomycin;  aminoglycoside antibiotic;  plazomicin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3272	UPDATE	PNGM-1	 carbapenem;  penam;  cephalosporin;  PNGM beta-lactamase;  antibiotic inactivation; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1925	UPDATE	MexB	 sulfonamide antibiotic;  penem;  panipenem;  tetracycline antibiotic;  clavulanic acid;  meropenem;  antibiotic efflux;  resistance-nodulation-cell division (RND) antibiotic efflux pump;  aztreonam;  nalidixic acid;  aminocoumarin antibiotic;  cephalosporin;  macrolide antibiotic;  carbapenem;  ceftazidime;  ciprofloxacin;  cephamycin;  ceftriaxone;  amoxicillin-clavulanic acid;  colistin B;  colistin A;  peptide antibiotic;  diaminopyrimidine antibiotic;  ticarcillin;  ampicillin;  amoxicillin;  penam;  sulfamethoxazole;  novobiocin;  phenicol antibiotic;  efflux pump complex or subunit conferring antibiotic resistance;  trimethoprim-sulfamethoxazole;  tetracycline;  monobactam;  fluoroquinolone antibiotic;  erythromycin;  trimethoprim;  azithromycin;  chloramphenicol; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3270	UPDATE	dfrA18	 trimethoprim;  diaminopyrimidine antibiotic;  trimethoprim resistant dihydrofolate reductase dfr;  antibiotic target replacement; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3271	UPDATE	ICR-Mo	 peptide antibiotic;  antibiotic target alteration;  colistin B;  intrinsic colistin resistant phosphoethanolamine transferase;  colistin A; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1928	UPDATE	OXA-50	 penam;  antibiotic inactivation;  carbapenem;  cephalosporin;  cefalotin;  ampicillin;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1929	UPDATE	ACT-24	 antibiotic inactivation;  carbapenem;  penam;  ACT beta-lactamase;  cephalosporin;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
496	UPDATE	KPC-16	 antibiotic inactivation;  penam;  carbapenem;  cephalosporin;  monobactam;  KPC beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3278	UPDATE	Acinetobacter baumannii AbaQ	 efflux pump complex or subunit conferring antibiotic resistance;  fluoroquinolone antibiotic;  major facilitator superfamily (MFS) antibiotic efflux pump;  antibiotic efflux; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3474	UPDATE	OXA-340	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
833	UPDATE	CfxA5	 antibiotic inactivation;  cephamycin;  CfxA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3476	UPDATE	OXA-342	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3477	UPDATE	OXA-343	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3470	UPDATE	OXA-308	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3471	UPDATE	OXA-336	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3472	UPDATE	OXA-337	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3473	UPDATE	OXA-339	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
490	UPDATE	TEM-188	 penam;  antibiotic inactivation;  penem;  cephalosporin;  monobactam;  ampicillin;  TEM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
838	UPDATE	CTX-M-102	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
839	UPDATE	CMY-44	 antibiotic inactivation;  CMY beta-lactamase;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3478	UPDATE	OXA-344	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3479	UPDATE	OXA-345	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
491	UPDATE	PER-2	 penam;  antibiotic inactivation;  penem;  carbapenem;  cephalosporin;  PER beta-lactamase;  monobactam; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1365	UPDATE	AAC(6')-I30	 AAC(6');  antibiotic inactivation;  aminoglycoside antibiotic;  gentamicin A; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with gentamicin A
UPDATED category_aro_cvterm_id with 40942
UPDATED category_aro_accession with 3004015
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Gentamicin A is part of a complex of broad spectrum aminoglycoside antibiotics. Gentamicin inhibits protein synthesis, resulting in bacterial cell death.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3	UPDATE	Escherichia coli ompF with mutation conferring resistance to beta-lactam antibiotics	 penam;  reduced permeability to antibiotic;  penem;  carbapenem;  cephalosporin;  cefepime;  cephamycin;  General Bacterial Porin with reduced permeability to beta-lactams;  monobactam; 	model_description; model_param	"UPDATED model_description with Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
"
492	UPDATE	Clostridium butyricum catB	 antibiotic inactivation;  thiamphenicol;  chloramphenicol acetyltransferase (CAT);  azidamfenicol;  phenicol antibiotic;  chloramphenicol; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
359	UPDATE	TEM-112	 penam;  antibiotic inactivation;  penem;  cephalosporin;  monobactam;  ampicillin;  TEM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
493	UPDATE	TEM-84	 penam;  antibiotic inactivation;  penem;  cephalosporin;  monobactam;  ampicillin;  TEM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
24	UPDATE	fusB	 antibiotic target protection;  fusidic acid;  fusidane antibiotic;  Target protecting FusB-type protein conferring resistance to Fusidic acid; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_name with fusidane antibiotic
UPDATED category_aro_cvterm_id with 45735
UPDATED category_aro_accession with 3007153
UPDATED category_aro_class_name with Drug Class
UPDATED category_aro_description with A group of antibiotics possessing steroid rings or steroid-like structures.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
25	UPDATE	CTX-M-121	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5310	UPDATE	PDC-170	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
26	UPDATE	VEB-3	 antibiotic inactivation;  monobactam;  cephalosporin;  VEB beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3319	UPDATE	AAC(6')-Ian	 antibiotic inactivation;  AAC(6');  kanamycin A;  amikacin;  aminoglycoside antibiotic;  tobramycin; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with kanamycin A
UPDATED category_aro_cvterm_id with 35966
UPDATED category_aro_accession with 0000049
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.
UPDATED category_aro_name with amikacin
UPDATED category_aro_cvterm_id with 35932
UPDATED category_aro_accession with 0000013
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.
UPDATED category_aro_name with tobramycin
UPDATED category_aro_cvterm_id with 35969
UPDATED category_aro_accession with 0000052
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3318	UPDATE	ADC-60	 antibiotic inactivation;  cephalosporin;  ADC beta-lactamase without carbapenemase activity; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1267	UPDATE	QnrB40	 sparfloxacin;  norfloxacin;  quinolone resistance protein (qnr);  gatifloxacin;  levofloxacin;  antibiotic target protection;  ciprofloxacin;  fluoroquinolone antibiotic;  nalidixic acid;  moxifloxacin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
27	UPDATE	lnuA	 antibiotic inactivation;  lincosamide nucleotidyltransferase (LNU);  lincomycin;  lincosamide antibiotic;  pirlimycin; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with lincomycin
UPDATED category_aro_cvterm_id with 35964
UPDATED category_aro_accession with 0000046
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Lincomycin is a lincosamide antibiotic that comes from the actinomyces Streptomyces lincolnensis. It binds to the 23s portion of the 50S subunit of bacterial ribosomes and inhibit early elongation of peptide chain by inhibiting transpeptidase reaction.
UPDATED category_aro_name with pirlimycin
UPDATED category_aro_cvterm_id with 45751
UPDATED category_aro_accession with 3007169
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Pirlimycin is an experimental/veterinary lincosamide antibiotic. Although not approved for use in humans, pirlimycin is commonly used to treat mammary gland infections in cattle.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5489	UPDATE	PDC-36	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5488	UPDATE	PDC-359	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5487	UPDATE	PDC-358	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5486	UPDATE	PDC-357	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3313	UPDATE	ACT-8	 antibiotic inactivation;  carbapenem;  penam;  ACT beta-lactamase;  cephalosporin;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5484	UPDATE	PDC-355	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5483	UPDATE	PDC-354	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5482	UPDATE	PDC-353	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5481	UPDATE	PDC-351	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5480	UPDATE	PDC-350	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
784	UPDATE	AAC(6')-Iv	 antibiotic inactivation;  AAC(6');  kanamycin A;  amikacin;  aminoglycoside antibiotic;  tobramycin; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with kanamycin A
UPDATED category_aro_cvterm_id with 35966
UPDATED category_aro_accession with 0000049
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.
UPDATED category_aro_name with amikacin
UPDATED category_aro_cvterm_id with 35932
UPDATED category_aro_accession with 0000013
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.
UPDATED category_aro_name with tobramycin
UPDATED category_aro_cvterm_id with 35969
UPDATED category_aro_accession with 0000052
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
785	UPDATE	OXY-2-9	 penam;  OXY beta-lactamase;  cephalosporin;  antibiotic inactivation;  monobactam; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
786	UPDATE	vanH gene in vanO cluster	 glycopeptide antibiotic;  glycopeptide resistance gene cluster;  vanH;  vancomycin;  antibiotic target alteration; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with vancomycin
UPDATED category_aro_cvterm_id with 35947
UPDATED category_aro_accession with 0000028
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.
UPDATED param_value with 200
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
787	UPDATE	dfrA23	 trimethoprim;  diaminopyrimidine antibiotic;  trimethoprim resistant dihydrofolate reductase dfr;  antibiotic target replacement; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5249	UPDATE	PDC-111	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
781	UPDATE	QnrB25	 sparfloxacin;  norfloxacin;  quinolone resistance protein (qnr);  gatifloxacin;  levofloxacin;  antibiotic target protection;  ciprofloxacin;  fluoroquinolone antibiotic;  nalidixic acid;  moxifloxacin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
782	UPDATE	OXA-63	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
783	UPDATE	NDM-1	 penam;  antibiotic inactivation;  imipenem;  cephamycin;  carbapenem;  cephalosporin;  NDM beta-lactamase;  amoxicillin;  clavulanic acid;  meropenem;  amoxicillin-clavulanic acid;  ertapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1726	UPDATE	FOX-4	 antibiotic inactivation;  cephamycin;  cephalosporin;  FOX beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1727	UPDATE	SHV-73	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  SHV beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1724	UPDATE	vanH gene in vanM cluster	 vanH;  glycopeptide resistance gene cluster;  teicoplanin;  glycopeptide antibiotic;  antibiotic target alteration;  vancomycin; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with vancomycin
UPDATED category_aro_cvterm_id with 35947
UPDATED category_aro_accession with 0000028
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.
UPDATED category_aro_name with teicoplanin
UPDATED category_aro_cvterm_id with 35948
UPDATED category_aro_accession with 0000029
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Teicoplanin is a glycopeptide antibiotic used in the prophylaxis and treatment of serious infections caused by Gram-positive bacteria. Teicoplanin has a unique acyl-aliphatic chain, and binds to cell wall precursors to inhibit transglycosylation  and transpeptidation.
UPDATED param_value with 200
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5246	UPDATE	PDC-108	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
788	UPDATE	SHV-46	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  SHV beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
789	UPDATE	IMP-43	 penam;  antibiotic inactivation;  penem;  carbapenem;  cephalosporin;  IMP beta-lactamase;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1720	UPDATE	tap	 tetracycline antibiotic;  efflux pump complex or subunit conferring antibiotic resistance;  major facilitator superfamily (MFS) antibiotic efflux pump;  tetracycline;  antibiotic efflux; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1721	UPDATE	Mycobacterium leprae folP with mutation conferring resistance to dapsone	 antibiotic target alteration;  sulfone antibiotic;  dapsone resistant dihydropteroate synthase folP;  dapsone; 	model_description; model_param	"UPDATED model_description with Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
"
5627	UPDATE	PLA-3	 carbapenem;  antibiotic inactivation;  cephalosporin;  PLA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
729	UPDATE	CTX-M-8	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5626	UPDATE	PLA-2a	 carbapenem;  antibiotic inactivation;  cephalosporin;  PLA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5625	UPDATE	PLA-1	 carbapenem;  antibiotic inactivation;  cephalosporin;  PLA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5624	UPDATE	PFM-3	 carbapenem;  antibiotic inactivation;  PFM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
468	UPDATE	Erm(37)	 streptogramin A antibiotic;  antibiotic target alteration;  virginiamycin S2;  vernamycin C;  pristinamycin IC;  patricin B;  patricin A;  oleandomycin;  ostreogrycin B3;  macrolide antibiotic;  telithromycin;  tylosin;  lincosamide antibiotic;  dirithromycin;  clarithromycin;  clindamycin;  dalfopristin;  pristinamycin IB;  quinupristin;  pristinamycin IA;  Erm 23S ribosomal RNA methyltransferase;  virginiamycin M1;  madumycin II;  griseoviridin;  streptogramin B antibiotic;  lincomycin;  streptogramin antibiotic;  roxithromycin;  spiramycin;  azithromycin;  erythromycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5623	UPDATE	PFM-2	 carbapenem;  antibiotic inactivation;  PFM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4386	UPDATE	BlaB-25	 carbapenem;  penam;  antibiotic inactivation;  BlaB beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
60	UPDATE	QnrS6	 sparfloxacin;  norfloxacin;  quinolone resistance protein (qnr);  gatifloxacin;  levofloxacin;  antibiotic target protection;  ciprofloxacin;  fluoroquinolone antibiotic;  nalidixic acid;  moxifloxacin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3311	UPDATE	ACT-38	 antibiotic inactivation;  carbapenem;  penam;  ACT beta-lactamase;  cephalosporin;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
62	UPDATE	CMY-42	 antibiotic inactivation;  cephalosporin;  ceftazidime;  cephamycin;  CMY beta-lactamase;  cefoxitin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
63	UPDATE	AAC(6')-Ib	 AAC(6');  antibiotic inactivation;  aminoglycoside antibiotic;  plazomicin;  tobramycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
64	UPDATE	CMY-70	 antibiotic inactivation;  CMY beta-lactamase;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5621	UPDATE	PER-9	 penam;  antibiotic inactivation;  penem;  carbapenem;  cephalosporin;  PER beta-lactamase;  monobactam; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
66	UPDATE	SHV-41	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  SHV beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3310	UPDATE	ADC-11	 antibiotic inactivation;  cephalosporin;  ADC beta-lactamase without carbapenemase activity; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
68	UPDATE	TEM-132	 penam;  antibiotic inactivation;  penem;  cephalosporin;  monobactam;  ampicillin;  TEM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
69	UPDATE	aadA23	 antibiotic inactivation;  aminoglycoside antibiotic;  ANT(3'');  streptomycin;  spectinomycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5620	UPDATE	PER-8	 penam;  antibiotic inactivation;  penem;  carbapenem;  cephalosporin;  PER beta-lactamase;  monobactam; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5485	UPDATE	PDC-356	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
123	UPDATE	SHV-64	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  SHV beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1371	UPDATE	CTX-M-26	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1588	UPDATE	QnrB50	 sparfloxacin;  norfloxacin;  quinolone resistance protein (qnr);  gatifloxacin;  levofloxacin;  antibiotic target protection;  ciprofloxacin;  fluoroquinolone antibiotic;  nalidixic acid;  moxifloxacin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3312	UPDATE	Mycoplasma genitalium 23S rRNA mutations confers resistance to fluoroquinolone and macrolide antibiotics	 23S rRNA with mutation conferring resistance to macrolide antibiotics;  macrolide antibiotic;  moxifloxacin;  antibiotic target alteration;  fluoroquinolone antibiotic;  azithromycin; 	model_description; ARO_category; model_param	"UPDATED model_description with Ribosomal RNA (rRNA) Gene Variant Models (RVM) are similar to Protein Variant Models (PVM), i.e. detect  sequences based on their similarity to a curated reference sequence and secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles, except RVMs are designed to detect AMR acquired via mutation of genes encoding ribosomal RNAs (rRNA). RVMs include a rRNA reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTN bit-score above the curated BLASTN cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTN bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
UPDATED category_aro_name with fluoroquinolone antibiotic
UPDATED category_aro_cvterm_id with 35920
UPDATED category_aro_accession with 0000001
UPDATED category_aro_class_name with Drug Class
UPDATED category_aro_description with The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.
UPDATED category_aro_name with azithromycin
UPDATED category_aro_cvterm_id with 36297
UPDATED category_aro_accession with 3000158
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Azithromycin is a 15-membered macrolide and falls under the subclass of azalide. Like other macrolides, azithromycin binds bacterial ribosomes to inhibit protein synthesis. The nitrogen substitution at the C-9a position prevents its degradation.
UPDATED category_aro_name with moxifloxacin
UPDATED category_aro_cvterm_id with 35991
UPDATED category_aro_accession with 0000074
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.
UPDATED param_description with The BLASTN bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
"
1370	UPDATE	AAC(6')-Ib10	 AAC(6');  antibiotic inactivation;  aminoglycoside antibiotic; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1582	UPDATE	dfrA5	 trimethoprim;  diaminopyrimidine antibiotic;  trimethoprim resistant dihydrofolate reductase dfr;  antibiotic target replacement; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3315	UPDATE	ADC-30	 antibiotic inactivation;  cephalosporin;  ADC beta-lactamase without carbapenemase activity; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1580	UPDATE	catIII	 antibiotic inactivation;  thiamphenicol;  chloramphenicol acetyltransferase (CAT);  azidamfenicol;  phenicol antibiotic;  chloramphenicol; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1581	UPDATE	ACT-3	 antibiotic inactivation;  carbapenem;  penam;  ACT beta-lactamase;  cephalosporin;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1586	UPDATE	CTX-M-32	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
405	UPDATE	OXA-202	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1584	UPDATE	tet(41)	 tetracycline antibiotic;  efflux pump complex or subunit conferring antibiotic resistance;  major facilitator superfamily (MFS) antibiotic efflux pump;  tetracycline;  antibiotic efflux; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3314	UPDATE	ADC-10	 antibiotic inactivation;  cephalosporin;  ADC beta-lactamase without carbapenemase activity; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2433	UPDATE	lfrA	 efflux pump complex or subunit conferring antibiotic resistance;  fluoroquinolone antibiotic;  major facilitator superfamily (MFS) antibiotic efflux pump;  antibiotic efflux; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1038	UPDATE	cmlB1	 antibiotic efflux;  efflux pump complex or subunit conferring antibiotic resistance;  major facilitator superfamily (MFS) antibiotic efflux pump;  phenicol antibiotic;  chloramphenicol; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
404	UPDATE	OXA-217	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3317	UPDATE	ADC-59	 antibiotic inactivation;  cephalosporin;  ADC beta-lactamase without carbapenemase activity; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
508	UPDATE	tetA(P)	 tetracycline antibiotic;  efflux pump complex or subunit conferring antibiotic resistance;  major facilitator superfamily (MFS) antibiotic efflux pump;  tetracycline;  antibiotic efflux; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2432	UPDATE	Klebsiella pneumoniae OmpK35	 penam;  reduced permeability to antibiotic;  imipenem;  monobactam;  cefamandole;  penem;  benzylpenicillin;  cephalosporin;  carbapenem;  ceftazidime;  cefepime;  cephamycin;  General Bacterial Porin with reduced permeability to beta-lactams;  ampicillin;  cefalotin;  resistance by absence;  ceftriaxone;  cefoxitin;  ertapenem; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Knockout Models (PKM) reflect resistance by the absence of a gene product, most often deletion of a gene involved in antibiotic import, such as Vibrio cholerae OmpT. Like Protein Homolog Models (PHMs), PKMs include a reference sequence and a bitscore cut-off for detection using BLASTP but instead are designed to only report lack of detection under Perfect or Strict criteria. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff. This model type is still under development and not currently supported by the Resistance Gene Identifier (RGI) software.
UPDATED category_aro_name with imipenem
UPDATED category_aro_cvterm_id with 36309
UPDATED category_aro_accession with 3000170
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Imipenem is a broad-spectrum antibiotic and is usually taken with cilastatin, which prevents hydrolysis of imipenem by renal dehydropeptidase-I. It is resistant to hydrolysis by most other beta-lactamases. Notable exceptions are the KPC beta-lactamases and Ambler Class B enzymes.
UPDATED category_aro_name with ceftriaxone
UPDATED category_aro_cvterm_id with 35979
UPDATED category_aro_accession with 0000062
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Ceftriaxone is a third-generation cephalosporin antibiotic. The presence of an aminothiazolyl sidechain increases ceftriazone's resistance to beta-lactamases. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria.
UPDATED category_aro_name with benzylpenicillin
UPDATED category_aro_cvterm_id with 36976
UPDATED category_aro_accession with 3000632
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Benzylpenicillin, commonly referred to as penicillin G, is effective against both Gram-positive and Gram-negative bacteria. It is unstable in acid.
UPDATED category_aro_name with ceftazidime
UPDATED category_aro_cvterm_id with 35977
UPDATED category_aro_accession with 0000060
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.
UPDATED category_aro_name with cefepime
UPDATED category_aro_cvterm_id with 35976
UPDATED category_aro_accession with 0000059
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Cefepime (INN) is a fourth-generation cephalosporin antibiotic developed in 1994. It contains an aminothiazolyl group that decreases its affinity with beta-lactamases. Cefepime shows high binding affinity with penicillin-binding proteins and has an extended spectrum of activity against Gram-positive and Gram-negative bacteria, with greater activity against both Gram-negative and Gram-positive organisms than third-generation agents.
UPDATED category_aro_name with ampicillin
UPDATED category_aro_cvterm_id with 36981
UPDATED category_aro_accession with 3000637
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.
UPDATED category_aro_name with cefalotin
UPDATED category_aro_cvterm_id with 37084
UPDATED category_aro_accession with 3000704
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Cefalotin is a semisynthetic cephalosporin antibiotic activate against staphylococci. It is resistant to staphylococci beta-lactamases but hydrolyzed by enterobacterial beta-lactamases.
UPDATED category_aro_name with cefamandole
UPDATED category_aro_cvterm_id with 40926
UPDATED category_aro_accession with 3003999
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Cefamandole is a second-generation cephalosporin-class beta-lactam antibiotic.
UPDATED category_aro_name with cefoxitin
UPDATED category_aro_cvterm_id with 35927
UPDATED category_aro_accession with 0000008
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Cefoxitin is a cephamycin antibiotic often grouped with the second generation cephalosporins. Cefoxitin is bactericidal and acts by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. Cefoxitin's 7-alpha-methoxy group and 3' leaving group make it a poor substrate for most beta-lactamases.
UPDATED category_aro_name with ertapenem
UPDATED category_aro_cvterm_id with 35987
UPDATED category_aro_accession with 0000070
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Ertapenem is a carbapenem antibiotic and is highly resistant to beta-lactamases like other carbapenems. It inhibits bacterial cell wall synthesis.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1032	UPDATE	OXA-365	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
403	UPDATE	dfrA8	 trimethoprim;  diaminopyrimidine antibiotic;  trimethoprim resistant dihydrofolate reductase dfr;  antibiotic target replacement; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1030	UPDATE	vanZ gene in vanA cluster	 vanZ;  glycopeptide resistance gene cluster;  teicoplanin;  antibiotic target alteration;  vancomycin;  glycopeptide antibiotic; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3316	UPDATE	ADC-58	 antibiotic inactivation;  cephalosporin;  ADC beta-lactamase without carbapenemase activity; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
502	UPDATE	aadA17	 antibiotic inactivation;  aminoglycoside antibiotic;  ANT(3'');  streptomycin;  spectinomycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
503	UPDATE	CTX-M-69	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
500	UPDATE	OXA-164	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
501	UPDATE	AAC(3)-VIIIa	 antibiotic inactivation;  AAC(3);  aminoglycoside antibiotic;  neomycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1212	UPDATE	OXA-141	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1213	UPDATE	nalD	 sulfonamide antibiotic;  penem;  panipenem;  tetracycline antibiotic;  clavulanic acid;  meropenem;  antibiotic efflux;  resistance-nodulation-cell division (RND) antibiotic efflux pump;  aztreonam;  nalidixic acid;  aminocoumarin antibiotic;  cephalosporin;  macrolide antibiotic;  carbapenem;  ceftazidime;  ciprofloxacin;  cephamycin;  ceftriaxone;  amoxicillin-clavulanic acid;  colistin B;  protein(s) and two-component regulatory system modulating antibiotic efflux;  colistin A;  peptide antibiotic;  diaminopyrimidine antibiotic;  ticarcillin;  ampicillin;  amoxicillin;  penam;  sulfamethoxazole;  novobiocin;  phenicol antibiotic;  efflux pump complex or subunit conferring antibiotic resistance;  trimethoprim-sulfamethoxazole;  tetracycline;  monobactam;  fluoroquinolone antibiotic;  erythromycin;  trimethoprim;  azithromycin;  chloramphenicol; 	model_description; model_param	"UPDATED model_description with Protein Overexpression Models (POM) are similar to Protein Variant Models (PVM) in that they include a protein reference sequence, a curated BLASTP bitscore cut-off, and mapped resistance variants. Whereas PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, reporting only those with curated mutations conferring AMR, POMs are restricted to regulatory proteins and report both wild-type sequences and/or sequences with mutations leading to overexpression of efflux complexes. The former lead to efflux of antibiotics at basal levels, while the latter can confer clinical resistance. POMs include a protein reference sequence (often from wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Perfect RGI match is 100% identical to the wild-type reference protein sequence along its entire length, a Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value may or may not contain at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off may or may not contain at least one curated mutation from amongst the mapped resistance variants.
UPDATED param_description with A subtype of the insertion mutation detection model parameter used when a set of insertion mutations are reported in a nucleotide sequence format, encoded as [+]nt[position]:[nucleotides], for example +nt391:GG. Such mutations may be of variable length, possibly causing a frameshift but not causing premature termination or a functional knockout.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
"
1210	UPDATE	novA	 efflux pump complex or subunit conferring antibiotic resistance;  ATP-binding cassette (ABC) antibiotic efflux pump;  aminocoumarin antibiotic;  novobiocin;  antibiotic efflux; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
633	UPDATE	OXA-355	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1216	UPDATE	SHV-119	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  SHV beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
635	UPDATE	OXA-332	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
636	UPDATE	CFE-1	 antibiotic inactivation;  CMY beta-lactamase;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
637	UPDATE	OXY-6-2	 penam;  OXY beta-lactamase;  cephalosporin;  antibiotic inactivation;  monobactam; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
638	UPDATE	ACT-16	 antibiotic inactivation;  carbapenem;  penam;  ACT beta-lactamase;  cephalosporin;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
639	UPDATE	AAC(3)-IV	 antibiotic inactivation;  AAC(3);  aminoglycoside antibiotic;  plazomicin;  apramycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1218	UPDATE	TEM-219	 penam;  antibiotic inactivation;  penem;  cephalosporin;  monobactam;  ampicillin;  TEM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1219	UPDATE	vanR gene in vanN cluster	 glycopeptide antibiotic;  glycopeptide resistance gene cluster;  antibiotic target alteration;  vanR;  vancomycin; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with vancomycin
UPDATED category_aro_cvterm_id with 35947
UPDATED category_aro_accession with 0000028
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4245	UPDATE	ADC-177	 antibiotic inactivation;  cephalosporin;  ADC beta-lactamases pending classification for carbapenemase activity; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1647	UPDATE	MexI	 antibiotic efflux;  resistance-nodulation-cell division (RND) antibiotic efflux pump;  norfloxacin;  efflux pump complex or subunit conferring antibiotic resistance;  acriflavine;  tetracycline antibiotic;  fluoroquinolone antibiotic;  disinfecting agents and antiseptics;  tetracycline; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4378	UPDATE	BlaB-17	 carbapenem;  penam;  antibiotic inactivation;  BlaB beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1394	UPDATE	OXA-257	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5658	UPDATE	SHV-191	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  SHV beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5659	UPDATE	SIM-2	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  SIM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4372	UPDATE	BlaB-11	 carbapenem;  penam;  antibiotic inactivation;  BlaB beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
780	UPDATE	CARB-9	 penam;  antibiotic inactivation;  CARB beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4370	UPDATE	BlaB-1	 carbapenem;  penam;  antibiotic inactivation;  BlaB beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2416	UPDATE	abcA	 penam;  peptide antibiotic;  ATP-binding cassette (ABC) antibiotic efflux pump;  antibiotic efflux;  daptomycin;  cefotaxime;  efflux pump complex or subunit conferring antibiotic resistance;  cephalosporin;  moenomycin A1;  methicillin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4376	UPDATE	BlaB-15	 carbapenem;  penam;  antibiotic inactivation;  BlaB beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4377	UPDATE	BlaB-16	 carbapenem;  penam;  antibiotic inactivation;  BlaB beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5650	UPDATE	SGM-7	 carbapenem;  antibiotic inactivation;  SGM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4375	UPDATE	BlaB-14	 carbapenem;  penam;  antibiotic inactivation;  BlaB beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
987	UPDATE	CTX-M-4	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2899	UPDATE	Vibrio anguillarum chloramphenicol acetyltransferase	 antibiotic inactivation;  phenicol antibiotic;  chloramphenicol acetyltransferase (CAT);  chloramphenicol; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1728	UPDATE	OXA-42	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1291	UPDATE	TEM-177	 penam;  antibiotic inactivation;  penem;  cephalosporin;  monobactam;  ampicillin;  TEM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2895	UPDATE	Enterococcus faecium chloramphenicol acetyltransferase	 antibiotic inactivation;  phenicol antibiotic;  chloramphenicol acetyltransferase (CAT);  chloramphenicol; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2894	UPDATE	Streptococcus suis chloramphenicol acetyltransferase	 antibiotic inactivation;  phenicol antibiotic;  chloramphenicol acetyltransferase (CAT);  chloramphenicol; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2897	UPDATE	Enterococcus faecalis chloramphenicol acetyltransferase	 antibiotic inactivation;  phenicol antibiotic;  chloramphenicol acetyltransferase (CAT);  chloramphenicol; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1729	UPDATE	CTX-M-66	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2891	UPDATE	Alkalihalobacillus clausii chloramphenicol acetyltransferase	 antibiotic inactivation;  phenicol antibiotic;  chloramphenicol acetyltransferase (CAT);  chloramphenicol; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2890	UPDATE	Agrobacterium fabrum chloramphenicol acetyltransferase	 antibiotic inactivation;  phenicol antibiotic;  chloramphenicol acetyltransferase (CAT);  chloramphenicol; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2893	UPDATE	Campylobacter coli chloramphenicol acetyltransferase	 antibiotic inactivation;  phenicol antibiotic;  chloramphenicol acetyltransferase (CAT);  chloramphenicol; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1454	UPDATE	CMY-112	 antibiotic inactivation;  CMY beta-lactamase;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1455	UPDATE	IND-9	 carbapenem;  antibiotic inactivation;  IND beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1456	UPDATE	IMP-15	 penam;  antibiotic inactivation;  penem;  carbapenem;  cephalosporin;  IMP beta-lactamase;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1457	UPDATE	CTX-M-13	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1102	UPDATE	QnrB29	 sparfloxacin;  norfloxacin;  quinolone resistance protein (qnr);  gatifloxacin;  levofloxacin;  antibiotic target protection;  ciprofloxacin;  fluoroquinolone antibiotic;  nalidixic acid;  moxifloxacin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1103	UPDATE	CMY-17	 antibiotic inactivation;  CMY beta-lactamase;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1452	UPDATE	TEM-216	 penam;  antibiotic inactivation;  penem;  cephalosporin;  monobactam;  ampicillin;  TEM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1101	UPDATE	CTX-M-21	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1898	UPDATE	OXA-379	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1458	UPDATE	TEM-157	 penam;  antibiotic inactivation;  penem;  cephalosporin;  monobactam;  ampicillin;  TEM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5247	UPDATE	PDC-109	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1108	UPDATE	Enterococcus faecium liaS mutant conferring daptomycin resistance	 antibiotic efflux;  protein(s) and two-component regulatory system modulating antibiotic efflux;  peptide antibiotic;  antibiotic target alteration;  daptomycin resistant liaS;  daptomycin; 	model_description; model_param	"UPDATED model_description with Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
"
4830	UPDATE	OXA-491	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4080	UPDATE	DfrA36	 trimethoprim;  diaminopyrimidine antibiotic;  trimethoprim resistant dihydrofolate reductase dfr;  antibiotic target replacement; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4081	UPDATE	DfrA38	 trimethoprim;  diaminopyrimidine antibiotic;  trimethoprim resistant dihydrofolate reductase dfr;  antibiotic target replacement; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3869	UPDATE	PDC-240	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3868	UPDATE	PDC-44	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4085	UPDATE	dfr22	 trimethoprim;  diaminopyrimidine antibiotic;  trimethoprim resistant dihydrofolate reductase dfr;  antibiotic target replacement; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
654	UPDATE	dfrA26	 trimethoprim;  diaminopyrimidine antibiotic;  trimethoprim resistant dihydrofolate reductase dfr;  antibiotic target replacement; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3863	UPDATE	PDC-59	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1722	UPDATE	TEM-184	 penam;  antibiotic inactivation;  penem;  cephalosporin;  monobactam;  ampicillin;  TEM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3861	UPDATE	PDC-54	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3860	UPDATE	PDC-43	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3867	UPDATE	PDC-52	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3866	UPDATE	PDC-56	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3865	UPDATE	PDC-67	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1723	UPDATE	IMP-44	 penam;  antibiotic inactivation;  penem;  carbapenem;  cephalosporin;  IMP beta-lactamase;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
322	UPDATE	FEZ-1	 carbapenem;  FEZ beta-lactamase;  cephalosporin;  antibiotic inactivation;  penam; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3837	UPDATE	Mycobacterium tuberculosis ethA mutations conferring resistance to prothionamide	 thioamide antibiotic;  antibiotic target alteration;  prothionamide resistant ethA; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
DELETED 40958
UPDATED category_aro_name with thioamide antibiotic
UPDATED category_aro_cvterm_id with 45738
UPDATED category_aro_accession with 3007156
UPDATED category_aro_class_name with Drug Class
UPDATED category_aro_description with A group of antibiotics possessing the thioamide functional group.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A subtype of the insertion mutation detection model parameter used when a set of insertion mutations are reported in a nucleotide sequence format, encoded as [+]nt[position]:[nucleotides], for example +nt391:GG. Such mutations may be of variable length, possibly causing a frameshift but not causing premature termination or a functional knockout.
UPDATED param_description with A subtype of the deletion mutation detection model parameter used when a set of deletion mutations are reported in a nucleotide sequence format, encoded as [-]nt[position]:[nucleotides], for example -nt25:T.
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
UPDATED param_description with A set of nucleotide or amino acid substitutions that are all required to confer resistance to an antibiotic drug or drug class, encoded as: [wild-type 1][position 1][mutation 1],[wild-type 2][position 2][mutation 2], etc. For example, D63Y,T142K.
UPDATED param_description with A nucleotide substitution resulting in a change from an amino acid codon to a STOP codon, encoded as [wild type amino acid][position][STOP], for example Q42STOP.
"
5243	UPDATE	PDC-103	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5242	UPDATE	PDC-102	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
467	UPDATE	CARB-3	 penam;  antibiotic inactivation;  CARB beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1577	UPDATE	AAC(6')-32	 antibiotic inactivation;  AAC(6');  amikacin;  aminoglycoside antibiotic;  gentamicin A;  tobramycin; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with amikacin
UPDATED category_aro_cvterm_id with 35932
UPDATED category_aro_accession with 0000013
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.
UPDATED category_aro_name with gentamicin A
UPDATED category_aro_cvterm_id with 40942
UPDATED category_aro_accession with 3004015
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Gentamicin A is part of a complex of broad spectrum aminoglycoside antibiotics. Gentamicin inhibits protein synthesis, resulting in bacterial cell death.
UPDATED category_aro_name with tobramycin
UPDATED category_aro_cvterm_id with 35969
UPDATED category_aro_accession with 0000052
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
323	UPDATE	aadA9	 antibiotic inactivation;  aminoglycoside antibiotic;  ANT(3'');  streptomycin;  spectinomycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5728	UPDATE	sepA	 efflux pump complex or subunit conferring antibiotic resistance;  small multidrug resistance (SMR) antibiotic efflux pump;  disinfecting agents and antiseptics;  antibiotic efflux; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5729	UPDATE	sdrM	 antibiotic efflux;  major facilitator superfamily (MFS) antibiotic efflux pump;  norfloxacin;  efflux pump complex or subunit conferring antibiotic resistance;  fluoroquinolone antibiotic;  disinfecting agents and antiseptics; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4909	UPDATE	OXA-583	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5722	UPDATE	VIM-73	 penam;  antibiotic inactivation;  penem;  carbapenem;  cephalosporin;  cephamycin;  VIM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5723	UPDATE	YEM-1	 carbapenem;  antibiotic inactivation;  YEM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5720	UPDATE	VIM-71	 penam;  antibiotic inactivation;  penem;  carbapenem;  cephalosporin;  cephamycin;  VIM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5721	UPDATE	VIM-72	 penam;  antibiotic inactivation;  penem;  carbapenem;  cephalosporin;  cephamycin;  VIM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5726	UPDATE	norC	 antibiotic efflux;  major facilitator superfamily (MFS) antibiotic efflux pump;  norfloxacin;  efflux pump complex or subunit conferring antibiotic resistance;  acriflavine;  ciprofloxacin;  fluoroquinolone antibiotic;  disinfecting agents and antiseptics; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5727	UPDATE	mdeA	 penam;  antibiotic efflux;  major facilitator superfamily (MFS) antibiotic efflux pump;  efflux pump complex or subunit conferring antibiotic resistance;  nalidixic acid;  kanamycin A;  tetracycline antibiotic;  acriflavine;  oxacillin;  ciprofloxacin;  ampicillin;  fluoroquinolone antibiotic;  aminoglycoside antibiotic;  disinfecting agents and antiseptics;  tetracycline; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5724	UPDATE	ZOG-1	 carbapenem;  antibiotic inactivation;  ZOG beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5636	UPDATE	RAHN-1	 antibiotic inactivation;  cephalosporin;  RAHN beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
466	UPDATE	CTX-M-76	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4832	UPDATE	OXA-494	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
320	UPDATE	Streptococcus pneumoniae PBP2x conferring resistance to amoxicillin	 penam;  cephamycin;  cephalosporin;  Penicillin-binding protein mutations conferring resistance to beta-lactam antibiotics;  antibiotic target alteration;  amoxicillin; 	model_description; model_param	"UPDATED model_description with Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
"
3917	UPDATE	CMY-157	 antibiotic inactivation;  CMY beta-lactamase;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4923	UPDATE	OXA-597	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3915	UPDATE	CMY-145	 antibiotic inactivation;  CMY beta-lactamase;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3914	UPDATE	CMY-125	 antibiotic inactivation;  CMY beta-lactamase;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3913	UPDATE	CMY-124	 antibiotic inactivation;  CMY beta-lactamase;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3912	UPDATE	CMY-141	 antibiotic inactivation;  CMY beta-lactamase;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3911	UPDATE	CMY-142	 antibiotic inactivation;  CMY beta-lactamase;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2137	UPDATE	Escherichia coli EF-Tu mutants conferring resistance to kirromycin	 antibiotic target alteration;  elfamycin antibiotic;  kirromycin;  elfamycin resistant EF-Tu; 	model_description; model_param	"UPDATED model_description with Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
"
1347	UPDATE	OXA-425	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4921	UPDATE	OXA-595	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3919	UPDATE	CMY-155	 antibiotic inactivation;  CMY beta-lactamase;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3918	UPDATE	CMY-171	 antibiotic inactivation;  CMY beta-lactamase;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4920	UPDATE	OXA-594	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4798	UPDATE	ORN-4	 carbapenem;  ORN beta-lactamase;  cephalosporin;  antibiotic inactivation; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4799	UPDATE	ORN-5	 carbapenem;  ORN beta-lactamase;  cephalosporin;  antibiotic inactivation; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1636	UPDATE	QnrB57	 sparfloxacin;  norfloxacin;  quinolone resistance protein (qnr);  gatifloxacin;  levofloxacin;  antibiotic target protection;  ciprofloxacin;  fluoroquinolone antibiotic;  nalidixic acid;  moxifloxacin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4794	UPDATE	OKP-D-1	 penam;  antibiotic inactivation;  OKP beta-lactamase;  cephalosporin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4795	UPDATE	ORN-1	 carbapenem;  ORN beta-lactamase;  cephalosporin;  antibiotic inactivation; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4973	UPDATE	OXA-652	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4797	UPDATE	ORN-3	 carbapenem;  ORN beta-lactamase;  cephalosporin;  antibiotic inactivation; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4790	UPDATE	OKP-B-40	 penam;  antibiotic inactivation;  OKP beta-lactamase;  cephalosporin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4791	UPDATE	OKP-B-41	 penam;  antibiotic inactivation;  OKP beta-lactamase;  cephalosporin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4792	UPDATE	OKP-B-45	 penam;  antibiotic inactivation;  OKP beta-lactamase;  cephalosporin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4793	UPDATE	OKP-C-1	 penam;  antibiotic inactivation;  OKP beta-lactamase;  cephalosporin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4152	UPDATE	ACT-61	 antibiotic inactivation;  carbapenem;  penam;  ACT beta-lactamase;  cephalosporin;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4153	UPDATE	ACT-62	 antibiotic inactivation;  carbapenem;  penam;  ACT beta-lactamase;  cephalosporin;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4150	UPDATE	ACT-59	 antibiotic inactivation;  carbapenem;  penam;  ACT beta-lactamase;  cephalosporin;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4151	UPDATE	ACT-60	 antibiotic inactivation;  carbapenem;  penam;  ACT beta-lactamase;  cephalosporin;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4156	UPDATE	ACT-65	 antibiotic inactivation;  carbapenem;  penam;  ACT beta-lactamase;  cephalosporin;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4157	UPDATE	ACT-66	 antibiotic inactivation;  carbapenem;  penam;  ACT beta-lactamase;  cephalosporin;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4154	UPDATE	ACT-63	 antibiotic inactivation;  carbapenem;  penam;  ACT beta-lactamase;  cephalosporin;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4155	UPDATE	ACT-64	 antibiotic inactivation;  carbapenem;  penam;  ACT beta-lactamase;  cephalosporin;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3844	UPDATE	AAC(6')-Ib-cr7	 antibiotic inactivation;  AAC(6')-Ib-cr;  kanamycin A;  ciprofloxacin;  fluoroquinolone antibiotic;  amikacin;  aminoglycoside antibiotic;  tobramycin; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with kanamycin A
UPDATED category_aro_cvterm_id with 35966
UPDATED category_aro_accession with 0000049
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.
UPDATED category_aro_name with amikacin
UPDATED category_aro_cvterm_id with 35932
UPDATED category_aro_accession with 0000013
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.
UPDATED category_aro_name with tobramycin
UPDATED category_aro_cvterm_id with 35969
UPDATED category_aro_accession with 0000052
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.
UPDATED category_aro_name with ciprofloxacin
UPDATED category_aro_cvterm_id with 35954
UPDATED category_aro_accession with 0000036
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4158	UPDATE	ACT-67	 antibiotic inactivation;  carbapenem;  penam;  ACT beta-lactamase;  cephalosporin;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4159	UPDATE	ACT-68	 antibiotic inactivation;  carbapenem;  penam;  ACT beta-lactamase;  cephalosporin;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
951	UPDATE	ACT-15	 antibiotic inactivation;  carbapenem;  penam;  ACT beta-lactamase;  cephalosporin;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
950	UPDATE	ErmX	 streptogramin A antibiotic;  antibiotic target alteration;  virginiamycin S2;  vernamycin C;  pristinamycin IC;  patricin B;  patricin A;  oleandomycin;  ostreogrycin B3;  macrolide antibiotic;  telithromycin;  tylosin;  lincosamide antibiotic;  dirithromycin;  clarithromycin;  clindamycin;  dalfopristin;  pristinamycin IB;  quinupristin;  pristinamycin IA;  Erm 23S ribosomal RNA methyltransferase;  virginiamycin M1;  madumycin II;  griseoviridin;  streptogramin B antibiotic;  lincomycin;  streptogramin antibiotic;  roxithromycin;  spiramycin;  azithromycin;  erythromycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1910	UPDATE	CTX-M-136	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
326	UPDATE	OXA-225	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
953	UPDATE	Enterococcus faecalis liaF mutant conferring daptomycin resistance	 antibiotic efflux;  protein(s) and two-component regulatory system modulating antibiotic efflux;  peptide antibiotic;  daptomycin resistant liaF;  antibiotic target alteration;  daptomycin; 	model_description; model_param	"UPDATED model_description with Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
UPDATED param_description with A subtype of the insertion mutation detection model parameter is used when a set of insertion mutations are reported in a peptide sequence format, encoded as [+][AAs][position range], for example +D345 or +MPL110-112.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
UPDATED param_description with A subtype of the deletion mutation detection model parameter used when a set of deletion mutations are reported in a peptide sequence format, encoded as [-][AAs][position range], for example -K527 or -QN517-518.
"
4034	UPDATE	PDC-376	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
216	UPDATE	LEN-9	 penam;  LEN beta-lactamase;  antibiotic inactivation;  penem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
217	UPDATE	vanX gene in vanA cluster	 antibiotic target alteration;  glycopeptide resistance gene cluster;  teicoplanin;  glycopeptide antibiotic;  vanX;  vancomycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_value with 200
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
214	UPDATE	SHV-121	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  SHV beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
215	UPDATE	bcrC	 peptide antibiotic;  undecaprenyl pyrophosphate related proteins;  bacitracin B;  bacitracin F;  bacitracin A;  antibiotic target alteration;  bacitracin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
212	UPDATE	Staphylococcus aureus parC conferring resistance to fluoroquinolones	 grepafloxacin;  trovafloxacin;  ofloxacin;  norfloxacin;  nalidixic acid;  lomefloxacin;  gatifloxacin;  sparfloxacin;  levofloxacin;  fluoroquinolone resistant parC;  antibiotic target alteration;  enoxacin;  ciprofloxacin;  pefloxacin;  fluoroquinolone antibiotic;  moxifloxacin; 	model_description; model_param	"UPDATED model_description with Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
"
213	UPDATE	OXA-21	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
210	UPDATE	SHV-35	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  SHV beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
211	UPDATE	TEM-206	 penam;  antibiotic inactivation;  penem;  cephalosporin;  monobactam;  ampicillin;  TEM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
983	UPDATE	GES-20	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  GES beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5009	UPDATE	OXA-697	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4036	UPDATE	PDC-231	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1186	UPDATE	OXA-327	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
218	UPDATE	npmA	 aminoglycoside antibiotic;  16S rRNA methyltransferase (A1408);  neomycin;  antibiotic target alteration;  amikacin;  ribostamycin;  gentamicin A; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with amikacin
UPDATED category_aro_cvterm_id with 35932
UPDATED category_aro_accession with 0000013
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.
UPDATED category_aro_name with ribostamycin
UPDATED category_aro_cvterm_id with 35940
UPDATED category_aro_accession with 0000021
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Ribostamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Ribostamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.
UPDATED category_aro_name with gentamicin A
UPDATED category_aro_cvterm_id with 40942
UPDATED category_aro_accession with 3004015
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Gentamicin A is part of a complex of broad spectrum aminoglycoside antibiotics. Gentamicin inhibits protein synthesis, resulting in bacterial cell death.
UPDATED category_aro_name with neomycin
UPDATED category_aro_cvterm_id with 35924
UPDATED category_aro_accession with 0000005
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
219	UPDATE	OKP-A-12	 penam;  antibiotic inactivation;  OKP beta-lactamase;  cephalosporin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4837	UPDATE	OXA-502	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2476	UPDATE	Halobacterium salinarum 16S rRNA mutation conferring resistance to pactamycin	 antibiotic target alteration;  16S rRNA with mutation conferring resistance to pactamycin;  pactamycin;  pactamycin-like antibiotic; 	model_description; ARO_category; model_param	"UPDATED model_description with Ribosomal RNA (rRNA) Gene Variant Models (RVM) are similar to Protein Variant Models (PVM), i.e. detect  sequences based on their similarity to a curated reference sequence and secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles, except RVMs are designed to detect AMR acquired via mutation of genes encoding ribosomal RNAs (rRNA). RVMs include a rRNA reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTN bit-score above the curated BLASTN cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTN bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_name with pactamycin-like antibiotic
UPDATED category_aro_cvterm_id with 45740
UPDATED category_aro_accession with 3007158
UPDATED category_aro_class_name with Drug Class
UPDATED category_aro_description with A group of antibiotics including pactamycin and its derivatives.
UPDATED param_description with The BLASTN bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
"
956	UPDATE	TEM-88	 penam;  antibiotic inactivation;  penem;  cephalosporin;  monobactam;  ampicillin;  TEM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
36	UPDATE	Mycobacterium leprae gyrA conferring resistance to fluoroquinolones	 grepafloxacin;  trovafloxacin;  ofloxacin;  norfloxacin;  nalidixic acid;  lomefloxacin;  gatifloxacin;  fluoroquinolone resistant gyrA;  levofloxacin;  sparfloxacin;  antibiotic target alteration;  enoxacin;  ciprofloxacin;  pefloxacin;  fluoroquinolone antibiotic;  moxifloxacin; 	model_description; model_param	"UPDATED model_description with Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
"
980	UPDATE	y56 beta-lactamase	 penam;  antibiotic inactivation;  BlaA beta-lactamase;  cephalosporin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
939	UPDATE	CTX-M-113	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4	UPDATE	SHV-52	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  SHV beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
324	UPDATE	QnrB54	 sparfloxacin;  norfloxacin;  quinolone resistance protein (qnr);  gatifloxacin;  levofloxacin;  antibiotic target protection;  ciprofloxacin;  fluoroquinolone antibiotic;  nalidixic acid;  moxifloxacin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4919	UPDATE	OXA-593	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3489	UPDATE	OXA-404	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3488	UPDATE	OXA-403	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4368	UPDATE	BEL-4	 penam;  monobactam;  cephalosporin;  antibiotic inactivation;  BEL beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3481	UPDATE	OXA-364	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3480	UPDATE	OXA-346	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3483	UPDATE	OXA-373	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3482	UPDATE	OXA-372	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3485	UPDATE	OXA-392	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3484	UPDATE	tva(A)	 Miscellaneous ABC-F subfamily ATP-binding cassette ribosomal protection proteins;  pleuromutilin antibiotic;  antibiotic target protection;  pleuromutilin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3487	UPDATE	OXA-401	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3486	UPDATE	OXA-400	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4563	UPDATE	CTX-M-234	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
929	UPDATE	GES-10	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  GES beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4561	UPDATE	CTX-M-232	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4560	UPDATE	CTX-M-231	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4567	UPDATE	CTX-M-238	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4566	UPDATE	CTX-M-237	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3649	UPDATE	Neisseria gonorrhoeae mtrR with mutation conferring resistance	 antibiotic efflux;  resistance-nodulation-cell division (RND) antibiotic efflux pump;  protein(s) and two-component regulatory system modulating antibiotic efflux;  macrolide antibiotic;  efflux pump complex or subunit conferring antibiotic resistance;  azithromycin;  erythromycin; 	model_description; model_param	"UPDATED model_description with Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
UPDATED param_description with A mutation in the promoter region of a gene which alters transcription of that gene. This is a pilot parameter in need of further documentation.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
"
4564	UPDATE	CTX-M-235	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3646	UPDATE	Neisseria gonorrhoeae 23S rRNA with mutation conferring resistance to azithromycin	 antibiotic target alteration;  23S rRNA with mutation conferring resistance to macrolide antibiotics;  macrolide antibiotic;  azithromycin; 	model_description; model_param	"UPDATED model_description with Ribosomal RNA (rRNA) Gene Variant Models (RVM) are similar to Protein Variant Models (PVM), i.e. detect  sequences based on their similarity to a curated reference sequence and secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles, except RVMs are designed to detect AMR acquired via mutation of genes encoding ribosomal RNAs (rRNA). RVMs include a rRNA reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTN bit-score above the curated BLASTN cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTN bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
UPDATED param_description with A mutation in the promoter region of a gene which alters transcription of that gene. This is a pilot parameter in need of further documentation.
UPDATED param_description with The BLASTN bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
"
3645	UPDATE	LEN-58	 penam;  LEN beta-lactamase;  antibiotic inactivation;  penem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3644	UPDATE	LEN-55	 penam;  LEN beta-lactamase;  antibiotic inactivation;  penem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3643	UPDATE	LEN-51	 penam;  LEN beta-lactamase;  antibiotic inactivation;  penem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3642	UPDATE	LEN-43	 penam;  LEN beta-lactamase;  antibiotic inactivation;  penem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3641	UPDATE	LEN-42	 penam;  LEN beta-lactamase;  antibiotic inactivation;  penem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3640	UPDATE	LEN-41	 penam;  LEN beta-lactamase;  antibiotic inactivation;  penem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2550	UPDATE	Clostridioides difficile gyrA conferring resistance to fluoroquinolones	 ofloxacin;  gatifloxacin;  fluoroquinolone resistant gyrA;  levofloxacin;  ciprofloxacin;  antibiotic target alteration;  fluoroquinolone antibiotic;  moxifloxacin; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
UPDATED category_aro_name with ofloxacin
UPDATED category_aro_cvterm_id with 37007
UPDATED category_aro_accession with 3000663
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Ofloxacin is a 6-fluoro, 7-piperazinyl quinolone with a methyl-substituted oxazine ring. It has a broad spectrum of activity including many enterobacteria and mycoplasma but most anaerobes are resistant.
UPDATED category_aro_name with levofloxacin
UPDATED category_aro_cvterm_id with 35988
UPDATED category_aro_accession with 0000071
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.
UPDATED category_aro_name with gatifloxacin
UPDATED category_aro_cvterm_id with 37003
UPDATED category_aro_accession with 3000659
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.
UPDATED category_aro_name with moxifloxacin
UPDATED category_aro_cvterm_id with 35991
UPDATED category_aro_accession with 0000074
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.
UPDATED category_aro_name with ciprofloxacin
UPDATED category_aro_cvterm_id with 35954
UPDATED category_aro_accession with 0000036
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
UPDATED param_description with A set of nucleotide or amino acid substitutions that are all required to confer resistance to an antibiotic drug or drug class, encoded as: [wild-type 1][position 1][mutation 1],[wild-type 2][position 2][mutation 2], etc. For example, D63Y,T142K.
"
2551	UPDATE	glycopeptide resistance gene cluster VanI	 glycopeptide antibiotic;  glycopeptide resistance gene cluster;  antibiotic target alteration;  vancomycin;  teicoplanin; 	model_description; ARO_category; model_param	"UPDATED model_description with Gene Cluster Meta-Models (PKM) are used to curate spatial clusters of individual genes within operons, such as for glycopeptide resistance gene clusters. The individual genes will have their own individual detection models (e.g. PHM, PVM, POM, etc.) while the PKM checks to see if all the component genes of the cluster have a Strict or Perfect hit and are ordered correctly within an operon. PKMs are encoded using the gene order parameter. This model type is still under development and not currently supported by the Resistance Gene Identifier (RGI) software.
UPDATED category_aro_name with vancomycin
UPDATED category_aro_cvterm_id with 35947
UPDATED category_aro_accession with 0000028
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.
UPDATED category_aro_name with teicoplanin
UPDATED category_aro_cvterm_id with 35948
UPDATED category_aro_accession with 0000029
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Teicoplanin is a glycopeptide antibiotic used in the prophylaxis and treatment of serious infections caused by Gram-positive bacteria. Teicoplanin has a unique acyl-aliphatic chain, and binds to cell wall precursors to inhibit transglycosylation  and transpeptidation.
UPDATED param_description with Spatial clusters of genes are encoded using the gene order parameter: [gene type]:[cvterm_id],[gene type]:[cvterm_id], etc. The gene type designations are: R = regulatory, C = core, A = accessory.
"
986	UPDATE	baeS	 antibiotic efflux;  resistance-nodulation-cell division (RND) antibiotic efflux pump;  protein(s) and two-component regulatory system modulating antibiotic efflux;  aminocoumarin antibiotic;  novobiocin;  efflux pump complex or subunit conferring antibiotic resistance;  aminoglycoside antibiotic; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
61	UPDATE	OXA-330	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2396	UPDATE	OXA-368	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2397	UPDATE	pgpB	 peptide antibiotic;  polymyxin B1;  polymyxin B;  lipid A phosphatase;  polymyxin B2;  polymyxin B3;  polymyxin B4;  antibiotic target alteration; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2394	UPDATE	Staphylococcus aureus menA with mutation conferring resistance to lysocin	 peptide antibiotic;  antibiotic target alteration;  Lysocin E;  lysocin resistant menA; 	model_description; model_param	"UPDATED model_description with Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
"
2395	UPDATE	apmA	 antibiotic inactivation;  aminoglycoside antibiotic;  apramycin;  amp acetyltransferase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2398	UPDATE	TEM-220	 penam;  antibiotic inactivation;  penem;  cephalosporin;  monobactam;  ampicillin;  TEM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
65	UPDATE	GES-21	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  GES beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5010	UPDATE	OXA-698	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2779	UPDATE	FosA6	 fosfomycin;  fosfomycin thiol transferase;  antibiotic inactivation;  phosphonic acid antibiotic; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_name with phosphonic acid antibiotic
UPDATED category_aro_cvterm_id with 45731
UPDATED category_aro_accession with 3007149
UPDATED category_aro_class_name with Drug Class
UPDATED category_aro_description with A group of antibiotics derived from phosphonic acids.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4899	UPDATE	OXA-572	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4898	UPDATE	OXA-569	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5014	UPDATE	OXA-702	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5015	UPDATE	OXA-703	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5016	UPDATE	OXA-704	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5017	UPDATE	OXA-705	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2770	UPDATE	kamB	 16S rRNA methyltransferase (A1408);  kanamycin A;  apramycin;  antibiotic target alteration;  aminoglycoside antibiotic;  neomycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2771	UPDATE	QepA2	 antibiotic efflux;  major facilitator superfamily (MFS) antibiotic efflux pump;  norfloxacin;  efflux pump complex or subunit conferring antibiotic resistance;  ciprofloxacin;  fluoroquinolone antibiotic;  moxifloxacin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4891	UPDATE	OXA-562	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4890	UPDATE	OXA-561	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2774	UPDATE	TMB-2	 antibiotic inactivation;  cephalosporin;  carbapenem;  ceftazidime;  cephamycin;  TMB beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2775	UPDATE	Pseudomonas aeruginosa soxR	 antibiotic target alteration;  tetracycline antibiotic;  antibiotic efflux;  ATP-binding cassette (ABC) antibiotic efflux pump;  major facilitator superfamily (MFS) antibiotic efflux pump;  resistance-nodulation-cell division (RND) antibiotic efflux pump;  norfloxacin;  cephalosporin;  cefalotin;  ciprofloxacin;  disinfecting agents and antiseptics;  tigecycline;  protein(s) and two-component regulatory system modulating antibiotic efflux;  rifampin;  ampicillin;  penam;  triclosan;  efflux pump complex or subunit conferring antibiotic resistance;  acriflavine;  glycylcycline;  fluoroquinolone antibiotic;  chloramphenicol;  phenicol antibiotic;  tetracycline;  rifamycin antibiotic; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4895	UPDATE	OXA-566	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4894	UPDATE	OXA-565	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3940	UPDATE	CMY-130	 antibiotic inactivation;  CMY beta-lactamase;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2800	UPDATE	cfrC	 florfenicol;  oxazolidinone antibiotic;  antibiotic target alteration;  streptogramin antibiotic;  chloramphenicol;  phenicol antibiotic;  Cfr 23S ribosomal RNA methyltransferase;  lincosamide antibiotic; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
312	UPDATE	OXA-167	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1858	UPDATE	OXA-387	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1859	UPDATE	QnrVC7	 sparfloxacin;  norfloxacin;  quinolone resistance protein (qnr);  gatifloxacin;  levofloxacin;  antibiotic target protection;  ciprofloxacin;  fluoroquinolone antibiotic;  nalidixic acid;  moxifloxacin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4419	UPDATE	CARB-33	 penam;  antibiotic inactivation;  CARB beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4418	UPDATE	CARB-32	 penam;  antibiotic inactivation;  CARB beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1850	UPDATE	FomB	 fosfomycin;  phosphonic acid antibiotic;  antibiotic inactivation;  Fom phosphotransferase family; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_name with phosphonic acid antibiotic
UPDATED category_aro_cvterm_id with 45731
UPDATED category_aro_accession with 3007149
UPDATED category_aro_class_name with Drug Class
UPDATED category_aro_description with A group of antibiotics derived from phosphonic acids.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4416	UPDATE	CARB-30	 penam;  antibiotic inactivation;  CARB beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1852	UPDATE	rmtF	 16S rRNA methyltransferase (G1405);  kanamycin A;  antibiotic target alteration;  astromicin;  aminoglycoside antibiotic;  gentamicin A; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with kanamycin A
UPDATED category_aro_cvterm_id with 35966
UPDATED category_aro_accession with 0000049
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.
UPDATED category_aro_name with astromicin
UPDATED category_aro_cvterm_id with 35922
UPDATED category_aro_accession with 0000003
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Astromicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Astromicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.
UPDATED category_aro_name with gentamicin A
UPDATED category_aro_cvterm_id with 40942
UPDATED category_aro_accession with 3004015
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Gentamicin A is part of a complex of broad spectrum aminoglycoside antibiotics. Gentamicin inhibits protein synthesis, resulting in bacterial cell death.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1853	UPDATE	OXA-20	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1854	UPDATE	rmtA	 kanamycin A;  aminoglycoside antibiotic;  isepamicin;  16S rRNA methyltransferase (G1405);  sisomicin;  arbekacin;  gentamicin B;  netilmicin;  antibiotic target alteration;  gentamicin C;  amikacin;  dibekacin;  G418;  tobramycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4412	UPDATE	CARB-26	 penam;  antibiotic inactivation;  CARB beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1856	UPDATE	QnrB20	 sparfloxacin;  norfloxacin;  quinolone resistance protein (qnr);  gatifloxacin;  levofloxacin;  antibiotic target protection;  ciprofloxacin;  fluoroquinolone antibiotic;  nalidixic acid;  moxifloxacin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1857	UPDATE	VIM-9	 penam;  antibiotic inactivation;  penem;  carbapenem;  cephalosporin;  cephamycin;  VIM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3842	UPDATE	AAC(6')-Ib-cr5	 antibiotic inactivation;  AAC(6')-Ib-cr;  kanamycin A;  ciprofloxacin;  fluoroquinolone antibiotic;  amikacin;  aminoglycoside antibiotic;  tobramycin; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with kanamycin A
UPDATED category_aro_cvterm_id with 35966
UPDATED category_aro_accession with 0000049
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.
UPDATED category_aro_name with amikacin
UPDATED category_aro_cvterm_id with 35932
UPDATED category_aro_accession with 0000013
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.
UPDATED category_aro_name with tobramycin
UPDATED category_aro_cvterm_id with 35969
UPDATED category_aro_accession with 0000052
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.
UPDATED category_aro_name with ciprofloxacin
UPDATED category_aro_cvterm_id with 35954
UPDATED category_aro_accession with 0000036
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
919	UPDATE	PER-1	 penam;  antibiotic inactivation;  penem;  carbapenem;  cephalosporin;  PER beta-lactamase;  monobactam; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
918	UPDATE	TEM-49	 penam;  antibiotic inactivation;  penem;  cephalosporin;  monobactam;  ampicillin;  TEM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4969	UPDATE	OXA-644	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4968	UPDATE	OXA-643	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
915	UPDATE	SHV-106	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  SHV beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
914	UPDATE	ANT(6)-Ia	 antibiotic inactivation;  streptomycin;  aminoglycoside antibiotic;  ANT(6); 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2178	UPDATE	glycopeptide resistance gene cluster VanO	 glycopeptide antibiotic;  glycopeptide resistance gene cluster;  antibiotic target alteration;  vancomycin; 	model_description; ARO_category; model_param	"UPDATED model_description with Gene Cluster Meta-Models (PKM) are used to curate spatial clusters of individual genes within operons, such as for glycopeptide resistance gene clusters. The individual genes will have their own individual detection models (e.g. PHM, PVM, POM, etc.) while the PKM checks to see if all the component genes of the cluster have a Strict or Perfect hit and are ordered correctly within an operon. PKMs are encoded using the gene order parameter. This model type is still under development and not currently supported by the Resistance Gene Identifier (RGI) software.
UPDATED category_aro_name with vancomycin
UPDATED category_aro_cvterm_id with 35947
UPDATED category_aro_accession with 0000028
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.
UPDATED param_description with Spatial clusters of genes are encoded using the gene order parameter: [gene type]:[cvterm_id],[gene type]:[cvterm_id], etc. The gene type designations are: R = regulatory, C = core, A = accessory.
"
4964	UPDATE	OXA-638	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
911	UPDATE	CMY-50	 antibiotic inactivation;  CMY beta-lactamase;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
910	UPDATE	rphA	 antibiotic inactivation;  rifampin;  rifapentine;  rifampin phosphotransferase;  rifabutin;  rifaximin;  rifamycin antibiotic; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
913	UPDATE	OXY-6-4	 penam;  OXY beta-lactamase;  cephalosporin;  antibiotic inactivation;  monobactam; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
912	UPDATE	LEN-13	 penam;  LEN beta-lactamase;  antibiotic inactivation;  penem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1421	UPDATE	TEM-85	 penam;  antibiotic inactivation;  penem;  cephalosporin;  monobactam;  ampicillin;  TEM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5450	UPDATE	PDC-32	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5694	UPDATE	VIM-45	 penam;  antibiotic inactivation;  penem;  carbapenem;  cephalosporin;  cephamycin;  VIM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5433	UPDATE	PDC-302	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5695	UPDATE	VIM-46	 penam;  antibiotic inactivation;  penem;  carbapenem;  cephalosporin;  cephamycin;  VIM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1109	UPDATE	CAU-1	 carbapenem;  penam;  CAU beta-lactamase;  antibiotic inactivation; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1423	UPDATE	TEM-15	 penam;  antibiotic inactivation;  penem;  cephalosporin;  monobactam;  ampicillin;  TEM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1933	UPDATE	SHV-160	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  SHV beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1932	UPDATE	IMP-32	 penam;  antibiotic inactivation;  penem;  carbapenem;  cephalosporin;  IMP beta-lactamase;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1931	UPDATE	TEM-150	 penam;  antibiotic inactivation;  penem;  cephalosporin;  monobactam;  ampicillin;  TEM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1589	UPDATE	PER-3	 penam;  antibiotic inactivation;  penem;  carbapenem;  cephalosporin;  PER beta-lactamase;  monobactam; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5128	UPDATE	OXA-826	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5287	UPDATE	PDC-15	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1935	UPDATE	Mycobacterium tuberculosis gyrA conferring resistance to fluoroquinolones	 grepafloxacin;  trovafloxacin;  ofloxacin;  norfloxacin;  nalidixic acid;  lomefloxacin;  gatifloxacin;  fluoroquinolone resistant gyrA;  levofloxacin;  sparfloxacin;  antibiotic target alteration;  enoxacin;  ciprofloxacin;  pefloxacin;  fluoroquinolone antibiotic;  moxifloxacin; 	model_description; model_param	"UPDATED model_description with Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
UPDATED param_description with A set of nucleotide or amino acid substitutions in different genes that are all required to confer resistance to an antibiotic drug or drug class, encoded as: [cvterm_id gene 1],[SNP 1],[SNP 2],etc+[cvterm_id gene 2],[SNP 1],[SNP 2],etc. For example: 39879,A90V,M94V+40052,D472H.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
UPDATED param_description with A set of nucleotide or amino acid substitutions that are all required to confer resistance to an antibiotic drug or drug class, encoded as: [wild-type 1][position 1][mutation 1],[wild-type 2][position 2][mutation 2], etc. For example, D63Y,T142K.
"
1934	UPDATE	lnuD	 antibiotic inactivation;  lincosamide nucleotidyltransferase (LNU);  lincomycin;  clindamycin;  lincosamide antibiotic; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with lincomycin
UPDATED category_aro_cvterm_id with 35964
UPDATED category_aro_accession with 0000046
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Lincomycin is a lincosamide antibiotic that comes from the actinomyces Streptomyces lincolnensis. It binds to the 23s portion of the 50S subunit of bacterial ribosomes and inhibit early elongation of peptide chain by inhibiting transpeptidase reaction.
UPDATED category_aro_name with clindamycin
UPDATED category_aro_cvterm_id with 35983
UPDATED category_aro_accession with 0000066
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Clindamycin is a lincosamide antibiotic that blocks A-site aminoacyl-tRNA binding. It is usually used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5124	UPDATE	OXA-821	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3368	UPDATE	emtA	 evernimicin;  orthosomycin antibiotic;  macrolide antibiotic;  non-erm 23S ribosomal RNA methyltransferase (G748);  antibiotic target alteration;  lincosamide antibiotic; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with evernimicin
UPDATED category_aro_cvterm_id with 45749
UPDATED category_aro_accession with 3007167
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Evernimicin is a veterinary oligosaccharide antibiotic of the orthosomycin group of orthoester antibiotics. Along with avilamycin, it exhibits activity against a variety of Gram-positive and -negative bacteria and is primarily used in livestock feed.
UPDATED category_aro_name with orthosomycin antibiotic
UPDATED category_aro_cvterm_id with 45748
UPDATED category_aro_accession with 3007166
UPDATED category_aro_class_name with Drug Class
UPDATED category_aro_description with Orthosomycins are a group of experimental/veterinary orthoester and oligosaccharide antibiotics that target the 70s ribosomal subunit. They are generally no longer considered potential clinical antibiotics, but continue to be used in livestock feed and for experimental purposes.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1939	UPDATE	AAC(6')-Ix	 antibiotic inactivation;  AAC(6');  kanamycin A;  amikacin;  aminoglycoside antibiotic;  tobramycin; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with kanamycin A
UPDATED category_aro_cvterm_id with 35966
UPDATED category_aro_accession with 0000049
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.
UPDATED category_aro_name with amikacin
UPDATED category_aro_cvterm_id with 35932
UPDATED category_aro_accession with 0000013
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.
UPDATED category_aro_name with tobramycin
UPDATED category_aro_cvterm_id with 35969
UPDATED category_aro_accession with 0000052
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1938	UPDATE	mtrD	 penam;  antibiotic efflux;  resistance-nodulation-cell division (RND) antibiotic efflux pump;  macrolide antibiotic;  efflux pump complex or subunit conferring antibiotic resistance;  penicillin;  azithromycin;  erythromycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5120	UPDATE	OXA-816	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5121	UPDATE	OXA-817	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5122	UPDATE	OXA-819	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5123	UPDATE	OXA-820	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
847	UPDATE	CTX-M-108	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
846	UPDATE	DHA-12	 antibiotic inactivation;  cephalosporin;  cephamycin;  DHA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
845	UPDATE	TEM-163	 penam;  antibiotic inactivation;  penem;  cephalosporin;  monobactam;  ampicillin;  TEM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
844	UPDATE	CMY-117	 antibiotic inactivation;  CMY beta-lactamase;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
843	UPDATE	QnrB14	 sparfloxacin;  norfloxacin;  quinolone resistance protein (qnr);  gatifloxacin;  levofloxacin;  antibiotic target protection;  ciprofloxacin;  fluoroquinolone antibiotic;  nalidixic acid;  moxifloxacin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
842	UPDATE	ugd	 pmr phosphoethanolamine transferase;  peptide antibiotic;  antibiotic target alteration;  polymyxin B; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with polymyxin B
UPDATED category_aro_cvterm_id with 36593
UPDATED category_aro_accession with 3000454
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Polymyxin B is mixture of mostly polymyxins B1 and B2, mainly used for resistant gram-negative infections. They are polypeptides with cationic detergent action on cell membranes.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3461	UPDATE	OXA-299	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3460	UPDATE	OXA-298	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1090	UPDATE	TEM-169	 penam;  antibiotic inactivation;  penem;  cephalosporin;  monobactam;  ampicillin;  TEM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5435	UPDATE	PDC-304	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
849	UPDATE	OXA-138	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
848	UPDATE	OKP-A-2	 penam;  antibiotic inactivation;  OKP beta-lactamase;  cephalosporin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
664	UPDATE	CMY-43	 antibiotic inactivation;  CMY beta-lactamase;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1429	UPDATE	SHV-60	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  SHV beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1583	UPDATE	QnrVC6	 sparfloxacin;  norfloxacin;  quinolone resistance protein (qnr);  gatifloxacin;  levofloxacin;  antibiotic target protection;  ciprofloxacin;  fluoroquinolone antibiotic;  nalidixic acid;  moxifloxacin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
459	UPDATE	CTX-M-94	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3366	UPDATE	pexA	 antibiotic efflux;  major facilitator superfamily (MFS) antibiotic efflux pump;  efflux pump complex or subunit conferring antibiotic resistance;  florfenicol;  phenicol antibiotic;  chloramphenicol; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5452	UPDATE	PDC-321	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3367	UPDATE	Staphylococcus aureus norA	 antibiotic efflux;  major facilitator superfamily (MFS) antibiotic efflux pump;  ofloxacin;  norfloxacin;  efflux pump complex or subunit conferring antibiotic resistance;  ciprofloxacin;  fluoroquinolone antibiotic;  enoxacin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2377	UPDATE	Escherichia coli PtsI with mutation conferring resistance to fosfomycin	 fosfomycin;  antibiotic-resistant ptsI phosphotransferase;  antibiotic target alteration;  phosphonic acid antibiotic; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_name with phosphonic acid antibiotic
UPDATED category_aro_cvterm_id with 45731
UPDATED category_aro_accession with 3007149
UPDATED category_aro_class_name with Drug Class
UPDATED category_aro_description with A group of antibiotics derived from phosphonic acids.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
"
1069	UPDATE	IMP-35	 penam;  antibiotic inactivation;  penem;  carbapenem;  cephalosporin;  IMP beta-lactamase;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4394	UPDATE	BlaB-32	 carbapenem;  penam;  antibiotic inactivation;  BlaB beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1587	UPDATE	OXA-10	 penam;  antibiotic inactivation;  avibactam;  OXA beta-lactamase;  cephalosporin;  ceftolozane-tazobactam;  ceftazidime-avibactam;  carbapenem;  ceftazidime;  tazobactam;  ceftolozane; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_description with Serine beta-lactamase inhibitor targeting class A, class C, and some class D enzymes.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2407	UPDATE	Capnocytophaga gingivalis gyrA conferring resistance to fluoroquinolones	 norfloxacin;  fluoroquinolone resistant gyrA;  levofloxacin;  ciprofloxacin;  antibiotic target alteration;  fluoroquinolone antibiotic; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
UPDATED category_aro_name with levofloxacin
UPDATED category_aro_cvterm_id with 35988
UPDATED category_aro_accession with 0000071
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.
UPDATED category_aro_name with norfloxacin
UPDATED category_aro_cvterm_id with 37006
UPDATED category_aro_accession with 3000662
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.
UPDATED category_aro_name with ciprofloxacin
UPDATED category_aro_cvterm_id with 35954
UPDATED category_aro_accession with 0000036
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
"
1585	UPDATE	CMY-73	 antibiotic inactivation;  CMY beta-lactamase;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5453	UPDATE	PDC-322	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1739	UPDATE	SHV-16	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  SHV beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1738	UPDATE	CTX-M-45	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2179	UPDATE	glycopeptide resistance gene cluster VanE	 glycopeptide antibiotic;  glycopeptide resistance gene cluster;  antibiotic target alteration;  vancomycin; 	model_description; ARO_category; model_param	"UPDATED model_description with Gene Cluster Meta-Models (PKM) are used to curate spatial clusters of individual genes within operons, such as for glycopeptide resistance gene clusters. The individual genes will have their own individual detection models (e.g. PHM, PVM, POM, etc.) while the PKM checks to see if all the component genes of the cluster have a Strict or Perfect hit and are ordered correctly within an operon. PKMs are encoded using the gene order parameter. This model type is still under development and not currently supported by the Resistance Gene Identifier (RGI) software.
UPDATED category_aro_name with vancomycin
UPDATED category_aro_cvterm_id with 35947
UPDATED category_aro_accession with 0000028
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.
UPDATED param_description with Spatial clusters of genes are encoded using the gene order parameter: [gene type]:[cvterm_id],[gene type]:[cvterm_id], etc. The gene type designations are: R = regulatory, C = core, A = accessory.
"
1068	UPDATE	AAC(6')-Ib3	 antibiotic inactivation;  AAC(6');  kanamycin A;  amikacin;  aminoglycoside antibiotic;  tobramycin; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with kanamycin A
UPDATED category_aro_cvterm_id with 35966
UPDATED category_aro_accession with 0000049
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.
UPDATED category_aro_name with amikacin
UPDATED category_aro_cvterm_id with 35932
UPDATED category_aro_accession with 0000013
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.
UPDATED category_aro_name with tobramycin
UPDATED category_aro_cvterm_id with 35969
UPDATED category_aro_accession with 0000052
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1731	UPDATE	mphB	 antibiotic inactivation;  macrolide phosphotransferase (MPH);  oleandomycin;  dirithromycin;  macrolide antibiotic;  telithromycin;  azithromycin;  roxithromycin;  spiramycin;  clarithromycin;  tylosin;  erythromycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1730	UPDATE	OXA-235	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1733	UPDATE	OXA-415	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1732	UPDATE	SHV-151	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  SHV beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5234	UPDATE	OXY-2-11	 penam;  OXY beta-lactamase;  cephalosporin;  antibiotic inactivation;  monobactam; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1734	UPDATE	IND-4	 carbapenem;  antibiotic inactivation;  IND beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1737	UPDATE	ANT(4')-Ia	 antibiotic inactivation;  aminoglycoside antibiotic;  ribostamycin;  plazomicin;  paromomycin;  kanamycin A;  gentamicin B;  lividomycin B;  ANT(4');  lividomycin A;  isepamicin;  G418;  neomycin;  tobramycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1736	UPDATE	GES-24	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  GES beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1039	UPDATE	dfrB3	 trimethoprim;  diaminopyrimidine antibiotic;  trimethoprim resistant dihydrofolate reductase dfr;  antibiotic target replacement; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3134	UPDATE	MCR-1.10	 peptide antibiotic;  MCR phosphoethanolamine transferase;  antibiotic target alteration;  colistin B;  colistin A; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1184	UPDATE	OXA-182	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5454	UPDATE	PDC-325	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
753	UPDATE	SMB-1	 SMB beta-lactamase;  carbapenem;  cephalosporin;  antibiotic inactivation;  penam; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3782	UPDATE	PDC-55	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
751	UPDATE	TEM-217	 penam;  antibiotic inactivation;  penem;  cephalosporin;  monobactam;  ampicillin;  TEM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
750	UPDATE	SHV-172	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  SHV beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
757	UPDATE	CMY-80	 antibiotic inactivation;  CMY beta-lactamase;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
756	UPDATE	Enterococcus faecium liaR mutant conferring daptomycin resistance	 antibiotic efflux;  protein(s) and two-component regulatory system modulating antibiotic efflux;  peptide antibiotic;  daptomycin resistant liaR;  antibiotic target alteration;  daptomycin; 	model_description; model_param	"UPDATED model_description with Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
"
755	UPDATE	KPC-9	 antibiotic inactivation;  penam;  carbapenem;  cephalosporin;  monobactam;  KPC beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3783	UPDATE	YajC	 penam;  antibiotic efflux;  triclosan;  rifampin;  resistance-nodulation-cell division (RND) antibiotic efflux pump;  efflux pump complex or subunit conferring antibiotic resistance;  disinfecting agents and antiseptics;  tetracycline antibiotic;  cephalosporin;  cefalotin;  tigecycline;  glycylcycline;  ampicillin;  fluoroquinolone antibiotic;  rifamycin antibiotic;  phenicol antibiotic;  tetracycline;  chloramphenicol; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
759	UPDATE	OCH-2	 penam;  antibiotic inactivation;  penem;  cephalosporin;  cephamycin;  monobactam;  OCH beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
509	UPDATE	FOX-1	 antibiotic inactivation;  cephamycin;  cephalosporin;  FOX beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3780	UPDATE	ADC-159	 antibiotic inactivation;  cephalosporin;  ADC beta-lactamase without carbapenemase activity; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5260	UPDATE	PDC-124	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1595	UPDATE	mecB	 penam;  methicillin resistant PBP2;  methicillin;  antibiotic target replacement; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with methicillin
UPDATED category_aro_cvterm_id with 35934
UPDATED category_aro_accession with 0000015
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Derived from penicillin to combat penicillin-resistance, methicillin is insensitive to beta-lactamases (also known as penicillinases) secreted by many penicillin-resistant bacteria. Methicillin is bactericidal, and acts by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
506	UPDATE	IMP-5	 penam;  antibiotic inactivation;  penem;  carbapenem;  cephalosporin;  IMP beta-lactamase;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3322	UPDATE	AAC(3)-IId	 antibiotic inactivation;  AAC(3);  aminoglycoside antibiotic;  gentamicin A; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with gentamicin A
UPDATED category_aro_cvterm_id with 40942
UPDATED category_aro_accession with 3004015
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Gentamicin A is part of a complex of broad spectrum aminoglycoside antibiotics. Gentamicin inhibits protein synthesis, resulting in bacterial cell death.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3781	UPDATE	PDC-65	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1591	UPDATE	CMY-64	 antibiotic inactivation;  CMY beta-lactamase;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1590	UPDATE	QnrB27	 sparfloxacin;  norfloxacin;  quinolone resistance protein (qnr);  gatifloxacin;  levofloxacin;  antibiotic target protection;  ciprofloxacin;  fluoroquinolone antibiotic;  nalidixic acid;  moxifloxacin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3076	UPDATE	dfrB4	 trimethoprim;  diaminopyrimidine antibiotic;  trimethoprim resistant dihydrofolate reductase dfr;  antibiotic target replacement; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
507	UPDATE	rosB	 antibiotic efflux;  polymyxin B1;  major facilitator superfamily (MFS) antibiotic efflux pump;  polymyxin B;  peptide antibiotic;  efflux pump complex or subunit conferring antibiotic resistance;  polymyxin B2;  polymyxin B3;  polymyxin B4; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5455	UPDATE	PDC-326	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1599	UPDATE	SHV-23	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  SHV beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1598	UPDATE	OXA-101	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3787	UPDATE	OmpA	 peptide antibiotic;  reduced permeability to antibiotic;  General Bacterial Porin with reduced permeability to peptide antibiotics;  polymyxin B;  defensin; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
DELETED 36017
UPDATED category_aro_name with peptide antibiotic
UPDATED category_aro_cvterm_id with 36192
UPDATED category_aro_accession with 3000053
UPDATED category_aro_class_name with Drug Class
UPDATED category_aro_description with Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.
UPDATED category_aro_name with General Bacterial Porin with reduced permeability to peptide antibiotics
UPDATED category_aro_cvterm_id with 41446
UPDATED category_aro_accession with 3004282
UPDATED category_aro_class_name with AMR Gene Family
UPDATED category_aro_description with These are GBPs that are associated with decreased susceptibility to peptide antibiotics either through mutations in the porin protein, absence of the porin protein, or expression of the porin protein.
UPDATED category_aro_name with polymyxin B
UPDATED category_aro_cvterm_id with 36593
UPDATED category_aro_accession with 3000454
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Polymyxin B is mixture of mostly polymyxins B1 and B2, mainly used for resistant gram-negative infections. They are polypeptides with cationic detergent action on cell membranes.
UPDATED category_aro_name with defensin
UPDATED category_aro_cvterm_id with 37037
UPDATED category_aro_accession with 3000693
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Defensins are natural cationic peptides that have antibiotic properties. It is part of the innate immune system of plants and animals.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1025	UPDATE	TEM-136	 penam;  antibiotic inactivation;  penem;  cephalosporin;  monobactam;  ampicillin;  TEM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1024	UPDATE	AAC(6')-Ib-SK	 AAC(6');  antibiotic inactivation;  aminoglycoside antibiotic; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1027	UPDATE	tet(H)	 tetracycline antibiotic;  efflux pump complex or subunit conferring antibiotic resistance;  major facilitator superfamily (MFS) antibiotic efflux pump;  tetracycline;  antibiotic efflux; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1031	UPDATE	APH(6)-Id	 antibiotic inactivation;  APH(6);  streptomycin;  aminoglycoside antibiotic; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5340	UPDATE	PDC-200	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3784	UPDATE	mlaF	 oxazolidinone antibiotic;  ATP-binding cassette (ABC) antibiotic efflux pump;  antibiotic efflux;  efflux pump complex or subunit conferring antibiotic resistance; 	model_description	"UPDATED model_description with Protein Knockout Models (PKM) reflect resistance by the absence of a gene product, most often deletion of a gene involved in antibiotic import, such as Vibrio cholerae OmpT. Like Protein Homolog Models (PHMs), PKMs include a reference sequence and a bitscore cut-off for detection using BLASTP but instead are designed to only report lack of detection under Perfect or Strict criteria. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff. This model type is still under development and not currently supported by the Resistance Gene Identifier (RGI) software.
"
1023	UPDATE	IMP-14	 penam;  antibiotic inactivation;  penem;  carbapenem;  cephalosporin;  IMP beta-lactamase;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1022	UPDATE	TEM-28	 penam;  antibiotic inactivation;  penem;  cephalosporin;  monobactam;  ampicillin;  TEM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1036	UPDATE	vanW gene in vanB cluster	 glycopeptide antibiotic;  glycopeptide resistance gene cluster;  antibiotic target alteration;  vancomycin;  vanW; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with vancomycin
UPDATED category_aro_cvterm_id with 35947
UPDATED category_aro_accession with 0000028
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.
UPDATED param_value with 50
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3785	UPDATE	mlaD	 oxazolidinone antibiotic;  ATP-binding cassette (ABC) antibiotic efflux pump;  antibiotic efflux;  efflux pump complex or subunit conferring antibiotic resistance; 	model_description	"UPDATED model_description with Protein Knockout Models (PKM) reflect resistance by the absence of a gene product, most often deletion of a gene involved in antibiotic import, such as Vibrio cholerae OmpT. Like Protein Homolog Models (PHMs), PKMs include a reference sequence and a bitscore cut-off for detection using BLASTP but instead are designed to only report lack of detection under Perfect or Strict criteria. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff. This model type is still under development and not currently supported by the Resistance Gene Identifier (RGI) software.
"
1029	UPDATE	CMY-102	 antibiotic inactivation;  CMY beta-lactamase;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1028	UPDATE	SHV-1	 antibiotic inactivation;  penam;  carbapenem;  cephalosporin;  ampicillin;  SHV beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1037	UPDATE	cmlA1	 antibiotic efflux;  efflux pump complex or subunit conferring antibiotic resistance;  major facilitator superfamily (MFS) antibiotic efflux pump;  phenicol antibiotic;  chloramphenicol; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3136	UPDATE	MCR-3.9	 peptide antibiotic;  MCR phosphoethanolamine transferase;  antibiotic target alteration;  colistin B;  colistin A; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1034	UPDATE	QnrA7	 sparfloxacin;  norfloxacin;  quinolone resistance protein (qnr);  gatifloxacin;  levofloxacin;  antibiotic target protection;  ciprofloxacin;  fluoroquinolone antibiotic;  nalidixic acid;  moxifloxacin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5456	UPDATE	PDC-327	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1035	UPDATE	Streptococcus pneumoniae PBP2b conferring resistance to amoxicillin	 penam;  cephamycin;  cephalosporin;  Penicillin-binding protein mutations conferring resistance to beta-lactam antibiotics;  antibiotic target alteration;  amoxicillin; 	model_description; model_param	"UPDATED model_description with Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
"
605	UPDATE	OXA-96	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
604	UPDATE	OXA-385	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4367	UPDATE	AXC-5	 AXC beta-lactamase;  carbapenem;  antibiotic inactivation; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
606	UPDATE	IMI-2	 carbapenem;  antibiotic inactivation;  IMI beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
601	UPDATE	dfrA20	 trimethoprim;  diaminopyrimidine antibiotic;  trimethoprim resistant dihydrofolate reductase dfr;  antibiotic target replacement; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1208	UPDATE	SHV-173	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  SHV beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
603	UPDATE	mdtG	 fosfomycin;  phosphonic acid antibiotic;  major facilitator superfamily (MFS) antibiotic efflux pump;  antibiotic efflux;  efflux pump complex or subunit conferring antibiotic resistance; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_name with phosphonic acid antibiotic
UPDATED category_aro_cvterm_id with 45731
UPDATED category_aro_accession with 3007149
UPDATED category_aro_class_name with Drug Class
UPDATED category_aro_description with A group of antibiotics derived from phosphonic acids.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4362	UPDATE	ANA-1	 carbapenem;  ANA beta-lactamase;  antibiotic inactivation; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1205	UPDATE	VIM-39	 penam;  antibiotic inactivation;  penem;  carbapenem;  cephalosporin;  cephamycin;  VIM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1207	UPDATE	DHA-13	 antibiotic inactivation;  cephalosporin;  cephamycin;  DHA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1206	UPDATE	QepA1	 antibiotic efflux;  major facilitator superfamily (MFS) antibiotic efflux pump;  norfloxacin;  efflux pump complex or subunit conferring antibiotic resistance;  ciprofloxacin;  fluoroquinolone antibiotic; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1201	UPDATE	CARB-22	 penam;  antibiotic inactivation;  CARB beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
608	UPDATE	OXA-361	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1203	UPDATE	Mycobacterium tuberculosis ndh with mutation conferring resistance to isoniazid	 isoniazid;  antibiotic target alteration;  isoniazid-like antibiotic;  antibiotic resistant ndh; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_name with isoniazid-like antibiotic
UPDATED category_aro_cvterm_id with 45734
UPDATED category_aro_accession with 3007152
UPDATED category_aro_class_name with Drug Class
UPDATED category_aro_description with A group of antibiotics containing isoniazid and its derivatives.
UPDATED param_description with A subtype of the insertion mutation detection model parameter used when a set of insertion mutations are reported in a nucleotide sequence format, encoded as [+]nt[position]:[nucleotides], for example +nt391:GG. Such mutations may be of variable length, possibly causing a frameshift but not causing premature termination or a functional knockout.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
"
1202	UPDATE	CTX-M-28	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5649	UPDATE	SGM-6	 carbapenem;  antibiotic inactivation;  SGM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5648	UPDATE	SGM-5	 carbapenem;  antibiotic inactivation;  SGM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1211	UPDATE	VIM-1	 penam;  antibiotic inactivation;  penem;  carbapenem;  cephalosporin;  cephamycin;  VIM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5457	UPDATE	PDC-328	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5641	UPDATE	RUB-1	 antibiotic inactivation;  cephalosporin;  RUB beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5640	UPDATE	RSD2-2	 RSD2 beta-lactamase;  carbapenem;  cephalosporin;  antibiotic inactivation; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5643	UPDATE	SFO-1	 carbapenem;  antibiotic inactivation;  SFO beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5642	UPDATE	SFC-1	 carbapenem;  antibiotic inactivation;  SFC beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5645	UPDATE	SGM-2	 carbapenem;  antibiotic inactivation;  SGM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5644	UPDATE	SGM-1	 carbapenem;  antibiotic inactivation;  SGM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5647	UPDATE	SGM-4	 carbapenem;  antibiotic inactivation;  SGM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4276	UPDATE	ADC-211	 antibiotic inactivation;  cephalosporin;  ADC beta-lactamases pending classification for carbapenemase activity; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1214	UPDATE	TEM-134	 penam;  antibiotic inactivation;  penem;  cephalosporin;  monobactam;  ampicillin;  TEM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1944	UPDATE	CTX-M-148	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2003	UPDATE	pmrA	 antibiotic efflux;  major facilitator superfamily (MFS) antibiotic efflux pump;  norfloxacin;  efflux pump complex or subunit conferring antibiotic resistance;  ciprofloxacin;  fluoroquinolone antibiotic; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1215	UPDATE	FosC	 fosfomycin;  phosphonic acid antibiotic;  antibiotic inactivation;  fosC phosphotransferase family; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_name with phosphonic acid antibiotic
UPDATED category_aro_cvterm_id with 45731
UPDATED category_aro_accession with 3007149
UPDATED category_aro_class_name with Drug Class
UPDATED category_aro_description with A group of antibiotics derived from phosphonic acids.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1447	UPDATE	OKP-A-10	 penam;  antibiotic inactivation;  OKP beta-lactamase;  cephalosporin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1110	UPDATE	LEN-19	 penam;  LEN beta-lactamase;  antibiotic inactivation;  penem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1113	UPDATE	ANT(6)-Ib	 antibiotic inactivation;  streptomycin;  aminoglycoside antibiotic;  ANT(6); 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1112	UPDATE	OXA-58	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5	UPDATE	dfrF	 trimethoprim;  diaminopyrimidine antibiotic;  trimethoprim resistant dihydrofolate reductase dfr;  antibiotic target replacement; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1114	UPDATE	ACT-17	 antibiotic inactivation;  carbapenem;  penam;  ACT beta-lactamase;  cephalosporin;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1441	UPDATE	Klebsiella aerogenes Omp36	 penam;  reduced permeability to antibiotic;  imipenem;  General Bacterial Porin with reduced permeability to beta-lactams;  penem;  carbapenem;  cephalosporin;  cefepime;  cephamycin;  monobactam;  cefpirome; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
UPDATED category_aro_name with cefpirome
UPDATED category_aro_cvterm_id with 42781
UPDATED category_aro_accession with 3004726
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Cefpirome is a fourth generation cephalosporin with activity against methicillin-susceptible Staphylococcus aureus, coagulase-negative staphylococci and viridans group streptococci, and in vitro activity towards Streptococcus pneumoniae.
UPDATED category_aro_name with imipenem
UPDATED category_aro_cvterm_id with 36309
UPDATED category_aro_accession with 3000170
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Imipenem is a broad-spectrum antibiotic and is usually taken with cilastatin, which prevents hydrolysis of imipenem by renal dehydropeptidase-I. It is resistant to hydrolysis by most other beta-lactamases. Notable exceptions are the KPC beta-lactamases and Ambler Class B enzymes.
UPDATED category_aro_name with cefepime
UPDATED category_aro_cvterm_id with 35976
UPDATED category_aro_accession with 0000059
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Cefepime (INN) is a fourth-generation cephalosporin antibiotic developed in 1994. It contains an aminothiazolyl group that decreases its affinity with beta-lactamases. Cefepime shows high binding affinity with penicillin-binding proteins and has an extended spectrum of activity against Gram-positive and Gram-negative bacteria, with greater activity against both Gram-negative and Gram-positive organisms than third-generation agents.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
"
1116	UPDATE	arr-2	 antibiotic inactivation;  rifampin;  rifapentine;  rifabutin;  rifampin ADP-ribosyltransferase (Arr);  rifaximin;  rifamycin antibiotic; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1119	UPDATE	EBR-1	 carbapenem;  penam;  cephalosporin;  EBR beta-lactamase;  antibiotic inactivation; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1118	UPDATE	OXA-2	 penam;  antibiotic inactivation;  cephalosporin;  carbapenem;  ceftazidime;  ampicillin;  amoxicillin;  OXA beta-lactamase;  meropenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2660	UPDATE	Enterobacter cloacae acrA	 penam;  antibiotic efflux;  triclosan;  rifampin;  resistance-nodulation-cell division (RND) antibiotic efflux pump;  efflux pump complex or subunit conferring antibiotic resistance;  disinfecting agents and antiseptics;  tetracycline antibiotic;  cephalosporin;  cefalotin;  tigecycline;  glycylcycline;  ampicillin;  fluoroquinolone antibiotic;  rifamycin antibiotic;  phenicol antibiotic;  tetracycline;  chloramphenicol; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1351	UPDATE	QnrVC1	 sparfloxacin;  norfloxacin;  quinolone resistance protein (qnr);  gatifloxacin;  levofloxacin;  antibiotic target protection;  ciprofloxacin;  fluoroquinolone antibiotic;  nalidixic acid;  moxifloxacin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1449	UPDATE	OXA-59	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1448	UPDATE	SHV-26	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  SHV beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4093	UPDATE	KPC-29	 antibiotic inactivation;  penam;  carbapenem;  cephalosporin;  monobactam;  KPC beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4092	UPDATE	KPC-27	 antibiotic inactivation;  penam;  carbapenem;  cephalosporin;  monobactam;  KPC beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4091	UPDATE	KPC-18	 antibiotic inactivation;  penam;  carbapenem;  cephalosporin;  monobactam;  KPC beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1350	UPDATE	TEM-93	 penam;  antibiotic inactivation;  penem;  cephalosporin;  monobactam;  ampicillin;  TEM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4097	UPDATE	KPC-30	 antibiotic inactivation;  penam;  carbapenem;  cephalosporin;  monobactam;  KPC beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4096	UPDATE	KPC-32	 antibiotic inactivation;  penam;  carbapenem;  cephalosporin;  monobactam;  KPC beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4095	UPDATE	KPC-31	 antibiotic inactivation;  penam;  carbapenem;  cephalosporin;  monobactam;  KPC beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4094	UPDATE	KPC-28	 antibiotic inactivation;  penam;  carbapenem;  cephalosporin;  monobactam;  KPC beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2401	UPDATE	Haemophilus parainfluenzae gyrA conferring resistance to fluoroquinolones	 antibiotic target alteration;  fluoroquinolone antibiotic;  fluoroquinolone resistant gyrA;  ciprofloxacin; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
UPDATED category_aro_name with ciprofloxacin
UPDATED category_aro_cvterm_id with 35954
UPDATED category_aro_accession with 0000036
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
"
4099	UPDATE	KPC-34	 antibiotic inactivation;  penam;  carbapenem;  cephalosporin;  monobactam;  KPC beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4098	UPDATE	KPC-33	 antibiotic inactivation;  penam;  carbapenem;  cephalosporin;  monobactam;  KPC beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
450	UPDATE	OXA-51	 penam;  antibiotic inactivation;  carbapenem;  BAL30072;  cephalosporin;  monobactam;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4826	UPDATE	OXA-307	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4857	UPDATE	OXA-522	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5737	UPDATE	salB	 retapamulin;  sal-type ABC-F protein;  virginiamycin M1;  pleuromutilin antibiotic;  tiamulin;  streptogramin A antibiotic;  lincomycin;  antibiotic target protection;  streptogramin antibiotic;  clindamycin;  lincosamide antibiotic; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5736	UPDATE	NDM-33	 penam;  antibiotic inactivation;  cephalosporin;  carbapenem;  ceftazidime;  NDM beta-lactamase;  ciprofloxacin;  cephamycin;  fluoroquinolone antibiotic; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5731	UPDATE	qacG	 efflux pump complex or subunit conferring antibiotic resistance;  antibiotic efflux;  small multidrug resistance (SMR) antibiotic efflux pump;  disinfecting agents and antiseptics;  benzalkonium chloride; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
463	UPDATE	CTX-M-30	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
489	UPDATE	Mycobacterium tuberculosis gidB mutation conferring resistance to streptomycin	 antibiotic target alteration;  streptomycin;  aminoglycoside antibiotic;  antibiotic resistant gidB; 	model_description; model_param	"UPDATED model_description with Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
UPDATED param_description with A subtype of the insertion mutation detection model parameter used when a set of insertion mutations are reported in a nucleotide sequence format, encoded as [+]nt[position]:[nucleotides], for example +nt391:GG. Such mutations may be of variable length, possibly causing a frameshift but not causing premature termination or a functional knockout.
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
UPDATED param_description with A nucleotide substitution resulting in a change from an amino acid codon to a STOP codon, encoded as [wild type amino acid][position][STOP], for example Q42STOP.
UPDATED param_description with A subtype of the deletion mutation detection model parameter used when a set of deletion mutations are reported in a nucleotide sequence format, encoded as [-]nt[position]:[nucleotides], for example -nt25:T.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
488	UPDATE	SHV-156	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  SHV beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
487	UPDATE	macB	 efflux pump complex or subunit conferring antibiotic resistance;  ATP-binding cassette (ABC) antibiotic efflux pump;  antibiotic efflux;  macrolide antibiotic;  erythromycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
486	UPDATE	cmlB	 antibiotic efflux;  efflux pump complex or subunit conferring antibiotic resistance;  major facilitator superfamily (MFS) antibiotic efflux pump;  phenicol antibiotic;  chloramphenicol; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
485	UPDATE	TEM-191	 penam;  antibiotic inactivation;  penem;  cephalosporin;  monobactam;  ampicillin;  TEM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
484	UPDATE	QnrB49	 sparfloxacin;  norfloxacin;  quinolone resistance protein (qnr);  gatifloxacin;  levofloxacin;  antibiotic target protection;  ciprofloxacin;  fluoroquinolone antibiotic;  nalidixic acid;  moxifloxacin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5739	UPDATE	salD	 retapamulin;  sal-type ABC-F protein;  virginiamycin M1;  pleuromutilin antibiotic;  tiamulin;  streptogramin A antibiotic;  lincomycin;  antibiotic target protection;  streptogramin antibiotic;  lincosamide antibiotic; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5738	UPDATE	salC	 retapamulin;  sal-type ABC-F protein;  virginiamycin M1;  pleuromutilin antibiotic;  tiamulin;  streptogramin A antibiotic;  lincomycin;  antibiotic target protection;  streptogramin antibiotic;  clindamycin;  lincosamide antibiotic; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
481	UPDATE	VIM-30	 penam;  antibiotic inactivation;  penem;  carbapenem;  cephalosporin;  cephamycin;  VIM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
480	UPDATE	GES-9	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  GES beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2009	UPDATE	aadA6	 antibiotic inactivation;  aminoglycoside antibiotic;  ANT(3'');  streptomycin;  spectinomycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5554	UPDATE	PDC-424	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4581	UPDATE	DHA-28	 antibiotic inactivation;  cephalosporin;  cephamycin;  DHA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
790	UPDATE	CMY-32	 antibiotic inactivation;  CMY beta-lactamase;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4580	UPDATE	DHA-27	 antibiotic inactivation;  cephalosporin;  cephamycin;  DHA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4725	UPDATE	KPC-62	 antibiotic inactivation;  penam;  carbapenem;  cephalosporin;  monobactam;  KPC beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4379	UPDATE	BlaB-18	 carbapenem;  penam;  antibiotic inactivation;  BlaB beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4583	UPDATE	DHA-4	 antibiotic inactivation;  cephalosporin;  cephamycin;  DHA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4724	UPDATE	KPC-61	 antibiotic inactivation;  penam;  carbapenem;  cephalosporin;  monobactam;  KPC beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1061	UPDATE	OXY-2-10	 penam;  OXY beta-lactamase;  cephalosporin;  antibiotic inactivation;  monobactam; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4582	UPDATE	DHA-29	 antibiotic inactivation;  cephalosporin;  cephamycin;  DHA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4727	UPDATE	KPC-64	 antibiotic inactivation;  penam;  carbapenem;  cephalosporin;  monobactam;  KPC beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3922	UPDATE	SHV-205	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  SHV beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3923	UPDATE	SHV-222	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  SHV beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3920	UPDATE	CMY-96	 antibiotic inactivation;  CMY beta-lactamase;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
723	UPDATE	SHV-72	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  SHV beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3926	UPDATE	SHV-201	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  SHV beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3927	UPDATE	SHV-212	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  SHV beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3924	UPDATE	SHV-198	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  SHV beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3925	UPDATE	SHV-195	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  SHV beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4721	UPDATE	KPC-58	 antibiotic inactivation;  penam;  carbapenem;  cephalosporin;  monobactam;  KPC beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3928	UPDATE	SHV-204	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  SHV beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3929	UPDATE	SHV-197	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  SHV beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
656	UPDATE	OXA-219	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3993	UPDATE	TEM-230	 penam;  antibiotic inactivation;  penem;  cephalosporin;  monobactam;  ampicillin;  TEM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5656	UPDATE	SHV-171	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  SHV beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4723	UPDATE	KPC-60	 antibiotic inactivation;  penam;  carbapenem;  cephalosporin;  monobactam;  KPC beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4789	UPDATE	OKP-B-36	 penam;  antibiotic inactivation;  OKP beta-lactamase;  cephalosporin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4373	UPDATE	BlaB-12	 carbapenem;  penam;  antibiotic inactivation;  BlaB beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4787	UPDATE	OKP-B-24	 penam;  antibiotic inactivation;  OKP beta-lactamase;  cephalosporin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4786	UPDATE	OKP-B-23	 penam;  antibiotic inactivation;  OKP beta-lactamase;  cephalosporin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4785	UPDATE	OKP-B-22	 penam;  antibiotic inactivation;  OKP beta-lactamase;  cephalosporin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4784	UPDATE	OKP-B-21	 penam;  antibiotic inactivation;  OKP beta-lactamase;  cephalosporin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4783	UPDATE	OKP-B-16	 penam;  antibiotic inactivation;  OKP beta-lactamase;  cephalosporin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4782	UPDATE	OKP-A-17	 penam;  antibiotic inactivation;  OKP beta-lactamase;  cephalosporin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4781	UPDATE	OHIO-1	 OHIO beta-lactamase;  antibiotic inactivation;  cephalosporin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4780	UPDATE	NDM-31	 antibiotic inactivation;  penam;  carbapenem;  cephalosporin;  cephamycin;  NDM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4371	UPDATE	BlaB-10	 carbapenem;  penam;  antibiotic inactivation;  BlaB beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4149	UPDATE	ACT-58	 antibiotic inactivation;  carbapenem;  penam;  ACT beta-lactamase;  cephalosporin;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4148	UPDATE	ACT-57	 antibiotic inactivation;  carbapenem;  penam;  ACT beta-lactamase;  cephalosporin;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4145	UPDATE	ACT-54	 antibiotic inactivation;  carbapenem;  penam;  ACT beta-lactamase;  cephalosporin;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5652	UPDATE	SHV-115	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  SHV beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4147	UPDATE	ACT-56	 antibiotic inactivation;  carbapenem;  penam;  ACT beta-lactamase;  cephalosporin;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4146	UPDATE	ACT-55	 antibiotic inactivation;  carbapenem;  penam;  ACT beta-lactamase;  cephalosporin;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4141	UPDATE	ACT-50	 antibiotic inactivation;  carbapenem;  penam;  ACT beta-lactamase;  cephalosporin;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4140	UPDATE	ACT-49	 antibiotic inactivation;  carbapenem;  penam;  ACT beta-lactamase;  cephalosporin;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4143	UPDATE	ACT-52	 antibiotic inactivation;  carbapenem;  penam;  ACT beta-lactamase;  cephalosporin;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4142	UPDATE	ACT-51	 antibiotic inactivation;  carbapenem;  penam;  ACT beta-lactamase;  cephalosporin;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3856	UPDATE	OXA-846	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3857	UPDATE	NDM-29	 antibiotic inactivation;  penam;  carbapenem;  cephalosporin;  cephamycin;  NDM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3854	UPDATE	PDC-47	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3855	UPDATE	PDC-51	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3852	UPDATE	PDC-66	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4374	UPDATE	BlaB-13	 carbapenem;  penam;  antibiotic inactivation;  BlaB beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3850	UPDATE	PDC-63	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3851	UPDATE	PDC-57	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5651	UPDATE	SHN-1	 carbapenem;  antibiotic inactivation;  SHN beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3858	UPDATE	PDC-11	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3859	UPDATE	PDC-62	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4497	UPDATE	CTX-M-168	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1487	UPDATE	SHV-48	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  SHV beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4822	UPDATE	OXA-114w	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5472	UPDATE	PDC-342	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2661	UPDATE	Escherichia coli acrA	 penam;  antibiotic efflux;  triclosan;  rifampin;  resistance-nodulation-cell division (RND) antibiotic efflux pump;  efflux pump complex or subunit conferring antibiotic resistance;  disinfecting agents and antiseptics;  tetracycline antibiotic;  cephalosporin;  cefalotin;  tigecycline;  glycylcycline;  ampicillin;  fluoroquinolone antibiotic;  rifamycin antibiotic;  phenicol antibiotic;  tetracycline;  chloramphenicol; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1062	UPDATE	SHV-71	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  SHV beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4814	UPDATE	OXA-114n	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1182	UPDATE	CTX-M-105	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
924	UPDATE	AAC(6')-33	 AAC(6');  antibiotic inactivation;  aminoglycoside antibiotic; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3391	UPDATE	MCR-3.12	 peptide antibiotic;  MCR phosphoethanolamine transferase;  antibiotic target alteration;  colistin B;  colistin A; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
16	UPDATE	KPC-10	 antibiotic inactivation;  penam;  carbapenem;  cephalosporin;  monobactam;  KPC beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5089	UPDATE	OXA-781	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3665	UPDATE	NDM-24	 antibiotic inactivation;  penam;  carbapenem;  cephalosporin;  cephamycin;  NDM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
900	UPDATE	tet(C)	 tetracycline antibiotic;  efflux pump complex or subunit conferring antibiotic resistance;  major facilitator superfamily (MFS) antibiotic efflux pump;  tetracycline;  antibiotic efflux; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2896	UPDATE	Staphylococcus intermedius chloramphenicol acetyltransferase	 antibiotic inactivation;  phenicol antibiotic;  chloramphenicol acetyltransferase (CAT);  chloramphenicol; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
199	UPDATE	SRT-1	 antibiotic inactivation;  cephalosporin;  SRT beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
198	UPDATE	TEM-138	 penam;  antibiotic inactivation;  penem;  cephalosporin;  monobactam;  ampicillin;  TEM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
195	UPDATE	CTX-M-58	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
194	UPDATE	SHV-61	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  SHV beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
197	UPDATE	CTX-M-56	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
196	UPDATE	Mycobacterium tuberculosis embB mutant conferring resistance to ethambutol	 antibiotic target alteration;  polyamine antibiotic;  ethambutol;  ethambutol resistant embB; 	model_description; model_param	"UPDATED model_description with Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
UPDATED param_description with A set of nucleotide or amino acid substitutions that are all required to confer resistance to an antibiotic drug or drug class, encoded as: [wild-type 1][position 1][mutation 1],[wild-type 2][position 2][mutation 2], etc. For example, D63Y,T142K.
"
191	UPDATE	OXA-199	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
190	UPDATE	OXA-195	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
193	UPDATE	TEM-121	 penam;  antibiotic inactivation;  penem;  cephalosporin;  monobactam;  ampicillin;  TEM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
192	UPDATE	CTX-M-38	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
19	UPDATE	IMP-2	 penam;  antibiotic inactivation;  penem;  carbapenem;  cephalosporin;  IMP beta-lactamase;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4558	UPDATE	CTX-M-229	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4559	UPDATE	CTX-M-230	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4556	UPDATE	CTX-M-227	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4557	UPDATE	CTX-M-228	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4554	UPDATE	CTX-M-225	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4555	UPDATE	CTX-M-226	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4552	UPDATE	CTX-M-223	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4553	UPDATE	CTX-M-224	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4550	UPDATE	CTX-M-221	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4551	UPDATE	CTX-M-222	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
457	UPDATE	OXA-93	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1106	UPDATE	NDM-5	 penam;  antibiotic inactivation;  piperacillin-tazobactam;  cephalosporin;  carbapenem;  ceftazidime;  NDM beta-lactamase;  cephamycin;  piperacillin;  tazobactam;  cefoxitin;  ertapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1107	UPDATE	PDC-2	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2124	UPDATE	Clostridioides difficile EF-Tu mutants conferring resistance to elfamycin	 antibiotic target alteration;  elfamycin antibiotic;  LFF571;  elfamycin resistant EF-Tu; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
UPDATED category_aro_name with LFF571
UPDATED category_aro_cvterm_id with 39998
UPDATED category_aro_accession with 3003414
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with LFF571 is a novel semi-synthetic thiopeptide antibiotic derived from GE2270. It has been shown to possess potent in vitro and in vivo activity against Gram-positive bacteria. It is hypothesized that it a translation inhibitor leading to cell death.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
"
1104	UPDATE	acrB	 penam;  antibiotic efflux;  triclosan;  rifampin;  resistance-nodulation-cell division (RND) antibiotic efflux pump;  efflux pump complex or subunit conferring antibiotic resistance;  disinfecting agents and antiseptics;  tetracycline antibiotic;  cephalosporin;  cefalotin;  tigecycline;  glycylcycline;  ampicillin;  fluoroquinolone antibiotic;  rifamycin antibiotic;  phenicol antibiotic;  tetracycline;  chloramphenicol; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
18	UPDATE	OXA-212	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2381	UPDATE	Staphylococcus aureus UhpT with mutation conferring resistance to fosfomycin	 fosfomycin;  phosphonic acid antibiotic;  antibiotic target alteration;  antibiotic-resistant UhpT; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_name with phosphonic acid antibiotic
UPDATED category_aro_cvterm_id with 45731
UPDATED category_aro_accession with 3007149
UPDATED category_aro_class_name with Drug Class
UPDATED category_aro_description with A group of antibiotics derived from phosphonic acids.
UPDATED param_description with A subtype of the insertion mutation detection model parameter used when a set of insertion mutations are reported in a nucleotide sequence format, encoded as [+]nt[position]:[nucleotides], for example +nt391:GG. Such mutations may be of variable length, possibly causing a frameshift but not causing premature termination or a functional knockout.
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
UPDATED param_description with A nucleotide substitution resulting in a change from an amino acid codon to a STOP codon, encoded as [wild type amino acid][position][STOP], for example Q42STOP.
UPDATED param_description with A subtype of the deletion mutation detection model parameter used when a set of deletion mutations are reported in a nucleotide sequence format, encoded as [-]nt[position]:[nucleotides], for example -nt25:T.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2380	UPDATE	Staphylococcus aureus GlpT with mutation conferring resistance to fosfomycin	 fosfomycin;  phosphonic acid antibiotic;  antibiotic target alteration;  antibiotic-resistant GlpT; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_name with phosphonic acid antibiotic
UPDATED category_aro_cvterm_id with 45731
UPDATED category_aro_accession with 3007149
UPDATED category_aro_class_name with Drug Class
UPDATED category_aro_description with A group of antibiotics derived from phosphonic acids.
UPDATED param_description with A subtype of the insertion mutation detection model parameter used when a set of insertion mutations are reported in a nucleotide sequence format, encoded as [+]nt[position]:[nucleotides], for example +nt391:GG. Such mutations may be of variable length, possibly causing a frameshift but not causing premature termination or a functional knockout.
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
UPDATED param_description with A nucleotide substitution resulting in a change from an amino acid codon to a STOP codon, encoded as [wild type amino acid][position][STOP], for example Q42STOP.
UPDATED param_description with A subtype of the deletion mutation detection model parameter used when a set of deletion mutations are reported in a nucleotide sequence format, encoded as [-]nt[position]:[nucleotides], for example -nt25:T.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2383	UPDATE	ANT(4')-Ib	 antibiotic inactivation;  aminoglycoside antibiotic;  isepamicin;  paromomycin;  kanamycin A;  gentamicin B;  lividomycin A;  lividomycin B;  ANT(4');  amikacin;  ribostamycin;  G418;  neomycin;  tobramycin; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with amikacin
UPDATED category_aro_cvterm_id with 35932
UPDATED category_aro_accession with 0000013
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1105	UPDATE	AAC(3)-VIa	 antibiotic inactivation;  aminoglycoside antibiotic;  gentamicin C;  AAC(3);  gentamicin B; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2387	UPDATE	Erm(47)	 quinupristin;  Erm 23S ribosomal RNA methyltransferase;  macrolide antibiotic;  streptogramin B antibiotic;  lincomycin;  streptogramin antibiotic;  antibiotic target alteration;  lincosamide antibiotic;  clindamycin;  spiramycin;  azithromycin;  erythromycin; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with quinupristin
UPDATED category_aro_cvterm_id with 36723
UPDATED category_aro_accession with 3000584
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Quinupristin is a type B streptogramin and a semisynthetic derivative of pristinamycin 1A. It is a component of the drug Synercid and interacts with the 50S subunit of the bacterial ribosome to inhibit protein synthesis.
UPDATED category_aro_name with streptogramin B antibiotic
UPDATED category_aro_cvterm_id with 35967
UPDATED category_aro_accession with 0000050
UPDATED category_aro_class_name with Drug Class
UPDATED category_aro_description with Streptogramin B antibiotics are are cyclic hepta- or hexa-depsipeptides.  Type B streptogramins block the peptide exit tunnel of the 50S bacterial ribosome. The general composition of group B streptogramins is 3-hydroxypicolinic acid-L-Thr-D-aminobutyric acid (or D-Ala)-L-Pro-L-Phe (or 4-N-,N-(dimethylamino)-L-Phe)-X-L-phenylglycine. Used alone, streptogramin B antibiotics are bacteriostatic, but is bactericidal when used with streptogramin A antibiotics.
UPDATED category_aro_name with lincomycin
UPDATED category_aro_cvterm_id with 35964
UPDATED category_aro_accession with 0000046
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Lincomycin is a lincosamide antibiotic that comes from the actinomyces Streptomyces lincolnensis. It binds to the 23s portion of the 50S subunit of bacterial ribosomes and inhibit early elongation of peptide chain by inhibiting transpeptidase reaction.
UPDATED category_aro_name with clindamycin
UPDATED category_aro_cvterm_id with 35983
UPDATED category_aro_accession with 0000066
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Clindamycin is a lincosamide antibiotic that blocks A-site aminoacyl-tRNA binding. It is usually used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria.
UPDATED category_aro_name with spiramycin
UPDATED category_aro_cvterm_id with 36295
UPDATED category_aro_accession with 3000156
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Spiramycin is a 16-membered macrolide and is natural product produced by Streptomyces ambofaciens. It binds to the 50S subunit of bacterial ribosomes and inhibits peptidyl transfer activity to disrupt protein synthesis.
UPDATED category_aro_name with azithromycin
UPDATED category_aro_cvterm_id with 36297
UPDATED category_aro_accession with 3000158
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Azithromycin is a 15-membered macrolide and falls under the subclass of azalide. Like other macrolides, azithromycin binds bacterial ribosomes to inhibit protein synthesis. The nitrogen substitution at the C-9a position prevents its degradation.
UPDATED category_aro_name with erythromycin
UPDATED category_aro_cvterm_id with 35925
UPDATED category_aro_accession with 0000006
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure/function processes critical for life or replication are inhibited.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2386	UPDATE	cipA	 dalfopristin;  thiamphenicol;  oxazolidinone antibiotic;  virginiamycin M1;  pleuromutilin antibiotic;  tiamulin;  madumycin II;  griseoviridin;  streptogramin A antibiotic;  lincomycin;  streptogramin antibiotic;  antibiotic target alteration;  lincosamide antibiotic;  azidamfenicol;  clindamycin;  phenicol antibiotic;  Cfr 23S ribosomal RNA methyltransferase;  chloramphenicol; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1450	UPDATE	Escherichia coli parC conferring resistance to fluoroquinolones	 grepafloxacin;  trovafloxacin;  ofloxacin;  norfloxacin;  nalidixic acid;  lomefloxacin;  gatifloxacin;  sparfloxacin;  levofloxacin;  fluoroquinolone resistant parC;  antibiotic target alteration;  enoxacin;  ciprofloxacin;  pefloxacin;  fluoroquinolone antibiotic;  moxifloxacin; 	model_description; model_param	"UPDATED model_description with Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
"
1451	UPDATE	MIR-17	 antibiotic inactivation;  monobactam;  cephalosporin;  MIR beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3580	UPDATE	DES-1	 penam;  antibiotic inactivation;  DES beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3581	UPDATE	DHA-9	 antibiotic inactivation;  cephalosporin;  cephamycin;  DHA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3582	UPDATE	ERP-1	 penam;  antibiotic inactivation;  ERP beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2768	UPDATE	MdtEF-TolC	 penam;  antibiotic efflux;  resistance-nodulation-cell division (RND) antibiotic efflux pump;  norfloxacin;  macrolide antibiotic;  efflux pump complex or subunit conferring antibiotic resistance;  oxacillin;  cloxacillin;  fluoroquinolone antibiotic;  erythromycin; 	model_description; model_param	"UPDATED model_description with Efflux Pump System Meta-Models (EPS) are dedicated to efflux complexes and their regulators, such as AcrAB-TolC. Using the efflux pump components parameter, this model type simply includes a list of detection models for each component of the complex. This model type is still under development and not currently supported by the Resistance Gene Identifier (RGI) software.
UPDATED param_description with Association of proteins within efflux protein complexes or regulatory networks are encoded by the efflux pump components parameter: model_id,model_id,model_id, etc.
"
5007	UPDATE	OXA-695	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3585	UPDATE	FONA-1	 penam;  antibiotic inactivation;  FONA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3586	UPDATE	FONA-2	 penam;  antibiotic inactivation;  FONA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3587	UPDATE	FONA-3	 penam;  antibiotic inactivation;  FONA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2763	UPDATE	MdtABC-TolC	 efflux pump complex or subunit conferring antibiotic resistance;  antibiotic efflux;  aminocoumarin antibiotic;  resistance-nodulation-cell division (RND) antibiotic efflux pump;  novobiocin; 	model_description; model_param	"UPDATED model_description with Efflux Pump System Meta-Models (EPS) are dedicated to efflux complexes and their regulators, such as AcrAB-TolC. Using the efflux pump components parameter, this model type simply includes a list of detection models for each component of the complex. This model type is still under development and not currently supported by the Resistance Gene Identifier (RGI) software.
UPDATED param_description with Association of proteins within efflux protein complexes or regulatory networks are encoded by the efflux pump components parameter: model_id,model_id,model_id, etc.
"
3589	UPDATE	FONA-5	 penam;  antibiotic inactivation;  FONA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2761	UPDATE	MexPQ-OpmE	 kitasamycin;  imipenem;  thiamphenicol;  resistance-nodulation-cell division (RND) antibiotic efflux pump;  rokitamycin;  antibiotic efflux;  trimethoprim;  macrolide antibiotic;  disinfecting agents and antiseptics;  carbapenem;  efflux pump complex or subunit conferring antibiotic resistance;  diaminopyrimidine antibiotic;  acriflavine;  tetracycline antibiotic;  chloramphenicol;  phenicol antibiotic;  tetracycline;  erythromycin; 	model_description; model_param	"UPDATED model_description with Efflux Pump System Meta-Models (EPS) are dedicated to efflux complexes and their regulators, such as AcrAB-TolC. Using the efflux pump components parameter, this model type simply includes a list of detection models for each component of the complex. This model type is still under development and not currently supported by the Resistance Gene Identifier (RGI) software.
UPDATED param_description with Association of proteins within efflux protein complexes or regulatory networks are encoded by the efflux pump components parameter: model_id,model_id,model_id, etc.
"
5008	UPDATE	OXA-696	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5797	UPDATE	Streptomyces lividans otr(A)	 tetracycline antibiotic;  tetracycline-resistant ribosomal protection protein;  antibiotic target protection;  tetracycline; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2766	UPDATE	EmrKY-TolC	 tetracycline antibiotic;  efflux pump complex or subunit conferring antibiotic resistance;  major facilitator superfamily (MFS) antibiotic efflux pump;  tetracycline;  antibiotic efflux; 	model_description; model_param	"UPDATED model_description with Efflux Pump System Meta-Models (EPS) are dedicated to efflux complexes and their regulators, such as AcrAB-TolC. Using the efflux pump components parameter, this model type simply includes a list of detection models for each component of the complex. This model type is still under development and not currently supported by the Resistance Gene Identifier (RGI) software.
UPDATED param_description with Association of proteins within efflux protein complexes or regulatory networks are encoded by the efflux pump components parameter: model_id,model_id,model_id, etc.
"
2765	UPDATE	EmrAB-TolC	 efflux pump complex or subunit conferring antibiotic resistance;  nalidixic acid;  major facilitator superfamily (MFS) antibiotic efflux pump;  fluoroquinolone antibiotic;  antibiotic efflux; 	model_description; model_param	"UPDATED model_description with Efflux Pump System Meta-Models (EPS) are dedicated to efflux complexes and their regulators, such as AcrAB-TolC. Using the efflux pump components parameter, this model type simply includes a list of detection models for each component of the complex. This model type is still under development and not currently supported by the Resistance Gene Identifier (RGI) software.
UPDATED param_description with Association of proteins within efflux protein complexes or regulatory networks are encoded by the efflux pump components parameter: model_id,model_id,model_id, etc.
"
2285	UPDATE	Staphylococcus aureus murA with mutation conferring resistance to fosfomycin	 antibiotic target alteration;  phosphonic acid antibiotic;  antibiotic-resistant murA transferase; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
DELETED 35944
UPDATED category_aro_name with phosphonic acid antibiotic
UPDATED category_aro_cvterm_id with 45731
UPDATED category_aro_accession with 3007149
UPDATED category_aro_class_name with Drug Class
UPDATED category_aro_description with A group of antibiotics derived from phosphonic acids.
UPDATED param_description with A nucleotide substitution resulting in a change from an amino acid codon to a STOP codon, encoded as [wild type amino acid][position][STOP], for example Q42STOP.
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
999	UPDATE	LEN-2	 penam;  LEN beta-lactamase;  antibiotic inactivation;  penem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4241	UPDATE	ADC-173	 antibiotic inactivation;  cephalosporin;  ADC beta-lactamases pending classification for carbapenemase activity; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2007	UPDATE	OXA-335	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3552	UPDATE	ARL-4	 penam;  antibiotic inactivation;  ARL Beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
902	UPDATE	OXA-92	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
903	UPDATE	APH(2'')-Ig	 antibiotic inactivation;  kanamycin A;  gentamicin B;  aminoglycoside antibiotic;  sisomicin;  arbekacin;  APH(2'');  netilmicin;  gentamicin C;  amikacin;  isepamicin;  gentamicin A;  tobramycin; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with gentamicin A
UPDATED category_aro_cvterm_id with 40942
UPDATED category_aro_accession with 3004015
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Gentamicin A is part of a complex of broad spectrum aminoglycoside antibiotics. Gentamicin inhibits protein synthesis, resulting in bacterial cell death.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1849	UPDATE	Mycobacterium tuberculosis tlyA mutations conferring resistance to aminoglycosides	 antibiotic target alteration;  capreomycin;  streptomycin;  aminoglycoside antibiotic;  Antibiotic resistant tlyA; 	model_description; model_param	"UPDATED model_description with Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
UPDATED param_description with A subtype of the insertion mutation detection model parameter used when a set of insertion mutations are reported in a nucleotide sequence format, encoded as [+]nt[position]:[nucleotides], for example +nt391:GG. Such mutations may be of variable length, possibly causing a frameshift but not causing premature termination or a functional knockout.
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
UPDATED param_description with A nucleotide substitution resulting in a change from an amino acid codon to a STOP codon, encoded as [wild type amino acid][position][STOP], for example Q42STOP.
UPDATED param_description with A subtype of the deletion mutation detection model parameter used when a set of deletion mutations are reported in a nucleotide sequence format, encoded as [-]nt[position]:[nucleotides], for example -nt25:T.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1848	UPDATE	CTX-M-75	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
906	UPDATE	CARB-21	 penam;  antibiotic inactivation;  CARB beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
907	UPDATE	fexA	 antibiotic efflux;  major facilitator superfamily (MFS) antibiotic efflux pump;  efflux pump complex or subunit conferring antibiotic resistance;  florfenicol;  phenicol antibiotic;  chloramphenicol; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
904	UPDATE	rmtB	 kanamycin A;  aminoglycoside antibiotic;  isepamicin;  16S rRNA methyltransferase (G1405);  sisomicin;  arbekacin;  gentamicin B;  netilmicin;  antibiotic target alteration;  gentamicin C;  amikacin;  dibekacin;  G418;  tobramycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4621	UPDATE	GES-38	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  GES beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4422	UPDATE	CARB-36	 penam;  antibiotic inactivation;  CARB beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1842	UPDATE	IMI-3	 carbapenem;  antibiotic inactivation;  IMI beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1841	UPDATE	OXA-76	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1840	UPDATE	CMY-59	 antibiotic inactivation;  CMY beta-lactamase;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1847	UPDATE	emrB	 efflux pump complex or subunit conferring antibiotic resistance;  nalidixic acid;  major facilitator superfamily (MFS) antibiotic efflux pump;  fluoroquinolone antibiotic;  antibiotic efflux; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4427	UPDATE	CARB-43	 penam;  antibiotic inactivation;  CARB beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1845	UPDATE	OXA-312	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1844	UPDATE	OXA-128	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4958	UPDATE	OXA-632	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4959	UPDATE	OXA-633	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1188	UPDATE	ErmV	 carbomycin;  kitasamycin;  Erm 23S ribosomal RNA methyltransferase;  oleandomycin;  chalcomycin;  macrolide antibiotic;  streptogramin antibiotic;  antibiotic target alteration;  lincosamide antibiotic;  celesticetin;  tylosin;  erythromycin; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with carbomycin
UPDATED category_aro_cvterm_id with 37627
UPDATED category_aro_accession with 3001228
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Produced by Streptomyces halstedii and Streptomyces thermotolerans.
UPDATED category_aro_name with kitasamycin
UPDATED category_aro_cvterm_id with 37626
UPDATED category_aro_accession with 3001227
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Kitasamycin is a macrolide antibiotic and is produced by Streptoverticillium kitasatoense. The drug has antimicrobial activity against a wide spectrum of pathogens.
UPDATED category_aro_name with oleandomycin
UPDATED category_aro_cvterm_id with 37247
UPDATED category_aro_accession with 3000867
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Oleandomycin is a 14-membered macrolide produced by Streptomyces antibioticus. It is ssimilar to erythromycin, and contains a desosamine amino sugar and an oleandrose sugar. It targets the 50S ribosomal subunit to prevent protein synthesis.
UPDATED category_aro_name with chalcomycin
UPDATED category_aro_cvterm_id with 37621
UPDATED category_aro_accession with 3001222
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Produced by Streptomyces bikiniensis.
UPDATED category_aro_name with celesticetin
UPDATED category_aro_cvterm_id with 37630
UPDATED category_aro_accession with 3001231
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Produced by Streptomyces caelestis, which also produces the macrolide niddamycin.
UPDATED category_aro_name with tylosin
UPDATED category_aro_cvterm_id with 36284
UPDATED category_aro_accession with 3000145
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Tylosin is a 16-membered macrolide, naturally produced by Streptomyces fradiae. It interacts with the bacterial ribosome 50S subunit to inhibit protein synthesis.
UPDATED category_aro_name with erythromycin
UPDATED category_aro_cvterm_id with 35925
UPDATED category_aro_accession with 0000006
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure/function processes critical for life or replication are inhibited.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4952	UPDATE	OXA-626	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4953	UPDATE	OXA-627	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4950	UPDATE	OXA-624	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4951	UPDATE	OXA-625	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4956	UPDATE	OXA-630	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4957	UPDATE	OXA-631	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4954	UPDATE	OXA-628	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
925	UPDATE	AAC(3)-IIb	 antibiotic inactivation;  AAC(3);  gentamicin B;  gentamicin C;  amikacin;  aminoglycoside antibiotic; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2614	UPDATE	mphE	 antibiotic inactivation;  macrolide phosphotransferase (MPH);  macrolide antibiotic;  erythromycin; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with erythromycin
UPDATED category_aro_cvterm_id with 35925
UPDATED category_aro_accession with 0000006
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure/function processes critical for life or replication are inhibited.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4626	UPDATE	GES-43	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  GES beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2147	UPDATE	Escherichia coli EF-Tu mutants conferring resistance to Enacyloxin IIa	 antibiotic target alteration;  elfamycin antibiotic;  enacyloxin IIa;  elfamycin resistant EF-Tu; 	model_description; model_param	"UPDATED model_description with Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
"
4627	UPDATE	GES-44	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  GES beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4082	UPDATE	DfrB9	 trimethoprim;  diaminopyrimidine antibiotic;  trimethoprim resistant dihydrofolate reductase dfr;  antibiotic target replacement; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3255	UPDATE	dfrA6	 trimethoprim;  diaminopyrimidine antibiotic;  trimethoprim resistant dihydrofolate reductase dfr;  antibiotic target replacement; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4718	UPDATE	KLUC-5	 antibiotic inactivation;  KLUC beta-lactamase;  cephalosporin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4083	UPDATE	DfrA39	 trimethoprim;  diaminopyrimidine antibiotic;  trimethoprim resistant dihydrofolate reductase dfr;  antibiotic target replacement; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3298	UPDATE	Klebsiella pneumoniae KpnG	 penem;  piperacillin;  antibiotic efflux;  imipenem;  major facilitator superfamily (MFS) antibiotic efflux pump;  norfloxacin;  cephalosporin;  macrolide antibiotic;  carbapenem;  ceftazidime;  spectinomycin;  ciprofloxacin;  gentamicin C;  streptomycin;  aminoglycoside antibiotic;  polymyxin B1;  polymyxin B;  peptide antibiotic;  ticarcillin;  ertapenem;  penam;  efflux pump complex or subunit conferring antibiotic resistance;  polymyxin B2;  polymyxin B3;  polymyxin B4;  fluoroquinolone antibiotic;  erythromycin;  azithromycin;  tobramycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3299	UPDATE	Klebsiella pneumoniae KpnH	 penem;  piperacillin;  antibiotic efflux;  imipenem;  major facilitator superfamily (MFS) antibiotic efflux pump;  norfloxacin;  cephalosporin;  macrolide antibiotic;  carbapenem;  ceftazidime;  spectinomycin;  ciprofloxacin;  gentamicin C;  streptomycin;  aminoglycoside antibiotic;  polymyxin B1;  polymyxin B;  peptide antibiotic;  ticarcillin;  ertapenem;  penam;  efflux pump complex or subunit conferring antibiotic resistance;  polymyxin B2;  polymyxin B3;  polymyxin B4;  fluoroquinolone antibiotic;  erythromycin;  azithromycin;  tobramycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5139	UPDATE	OXA-840	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5138	UPDATE	OXA-839	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3294	UPDATE	erm(32)	 antibiotic target alteration;  streptogramin antibiotic;  Erm 23S ribosomal RNA methyltransferase;  macrolide antibiotic;  lincosamide antibiotic; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5136	UPDATE	OXA-834	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5135	UPDATE	OXA-833	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3297	UPDATE	erm(46)	 Erm 23S ribosomal RNA methyltransferase;  macrolide antibiotic;  antibiotic target alteration;  streptogramin antibiotic;  clarithromycin;  erythromycin;  azithromycin;  lincosamide antibiotic; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with clarithromycin
UPDATED category_aro_cvterm_id with 35982
UPDATED category_aro_accession with 0000065
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Clarithromycin is a methyl derivative of erythromycin, sharing the 14-carbon macrolide ring. The antibiotic binds to the 50S subunit of the ribosome and is used to treat pharyngitis, tonsillitis, acute maxillary sinusitis, acute bacterial exacerbation of chronic bronchitis, pneumonia (especially atypical pneumonias associated with Chlamydia pneumoniae or TWAR), and skin structure infections.
UPDATED category_aro_name with azithromycin
UPDATED category_aro_cvterm_id with 36297
UPDATED category_aro_accession with 3000158
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Azithromycin is a 15-membered macrolide and falls under the subclass of azalide. Like other macrolides, azithromycin binds bacterial ribosomes to inhibit protein synthesis. The nitrogen substitution at the C-9a position prevents its degradation.
UPDATED category_aro_name with erythromycin
UPDATED category_aro_cvterm_id with 35925
UPDATED category_aro_accession with 0000006
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure/function processes critical for life or replication are inhibited.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3290	UPDATE	tet(53)	 antibiotic inactivation;  oxytetracycline;  tetracycline antibiotic;  minocycline;  tetracycline inactivation enzyme;  tetracycline; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with minocycline
UPDATED category_aro_cvterm_id with 36291
UPDATED category_aro_accession with 3000152
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Minocycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.
UPDATED category_aro_name with oxytetracycline
UPDATED category_aro_cvterm_id with 37012
UPDATED category_aro_accession with 3000668
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Oxytetracycline is a derivative of tetracycline with a 5-hydroxyl group. Its activity is similar to other tetracyclines.
UPDATED category_aro_name with tetracycline
UPDATED category_aro_cvterm_id with 35968
UPDATED category_aro_accession with 0000051
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5132	UPDATE	OXA-830	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3292	UPDATE	tet(54)	 tetracycline antibiotic;  antibiotic inactivation;  tetracycline inactivation enzyme;  oxytetracycline;  tetracycline; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with oxytetracycline
UPDATED category_aro_cvterm_id with 37012
UPDATED category_aro_accession with 3000668
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Oxytetracycline is a derivative of tetracycline with a 5-hydroxyl group. Its activity is similar to other tetracyclines.
UPDATED category_aro_name with tetracycline
UPDATED category_aro_cvterm_id with 35968
UPDATED category_aro_accession with 0000051
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5130	UPDATE	OXA-828	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
854	UPDATE	CMY-58	 antibiotic inactivation;  CMY beta-lactamase;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3453	UPDATE	OXA-289	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3450	UPDATE	OXA-285	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3451	UPDATE	OXA-287	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3456	UPDATE	OXA-293	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3457	UPDATE	OXA-294	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3454	UPDATE	OXA-291	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
853	UPDATE	OXA-160	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3458	UPDATE	OXA-295	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3459	UPDATE	OXA-297	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
858	UPDATE	IND-14	 carbapenem;  antibiotic inactivation;  IND beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
88	UPDATE	CMY-55	 antibiotic inactivation;  CMY beta-lactamase;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
721	UPDATE	OXA-28	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3293	UPDATE	tet(55)	 antibiotic inactivation;  oxytetracycline;  tetracycline antibiotic;  minocycline;  tetracycline inactivation enzyme;  tetracycline; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with minocycline
UPDATED category_aro_cvterm_id with 36291
UPDATED category_aro_accession with 3000152
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Minocycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.
UPDATED category_aro_name with oxytetracycline
UPDATED category_aro_cvterm_id with 37012
UPDATED category_aro_accession with 3000668
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Oxytetracycline is a derivative of tetracycline with a 5-hydroxyl group. Its activity is similar to other tetracyclines.
UPDATED category_aro_name with tetracycline
UPDATED category_aro_cvterm_id with 35968
UPDATED category_aro_accession with 0000051
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4088	UPDATE	KPC-23	 antibiotic inactivation;  penam;  carbapenem;  cephalosporin;  monobactam;  KPC beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3862	UPDATE	OXA-906	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4263	UPDATE	ADC-198	 antibiotic inactivation;  cephalosporin;  ADC beta-lactamases pending classification for carbapenemase activity; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4813	UPDATE	OXA-114m	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1187	UPDATE	OXA-248	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3864	UPDATE	OXA-850	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5229	UPDATE	OXA-945	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5228	UPDATE	OXA-943	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5223	UPDATE	OXA-938	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5222	UPDATE	OXA-937	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5221	UPDATE	OXA-935	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5220	UPDATE	OXA-932	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5227	UPDATE	OXA-942	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5226	UPDATE	OXA-941	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5225	UPDATE	OXA-940	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5224	UPDATE	OXA-939	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4265	UPDATE	ADC-200	 antibiotic inactivation;  cephalosporin;  ADC beta-lactamases pending classification for carbapenemase activity; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1554	UPDATE	norA	 antibiotic efflux;  major facilitator superfamily (MFS) antibiotic efflux pump;  norfloxacin;  efflux pump complex or subunit conferring antibiotic resistance;  acriflavine;  ciprofloxacin;  fluoroquinolone antibiotic;  disinfecting agents and antiseptics; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
740	UPDATE	QnrB21	 sparfloxacin;  norfloxacin;  quinolone resistance protein (qnr);  gatifloxacin;  levofloxacin;  antibiotic target protection;  ciprofloxacin;  fluoroquinolone antibiotic;  nalidixic acid;  moxifloxacin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
741	UPDATE	CfxA	 antibiotic inactivation;  flomoxef;  cefmetazole;  cephamycin;  cefotetan;  CfxA beta-lactamase;  cefoxitin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
742	UPDATE	AAC(3)-Id	 antibiotic inactivation;  AAC(3);  sisomicin;  gentamicin B;  astromicin;  gentamicin C;  aminoglycoside antibiotic; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
743	UPDATE	arr-3	 antibiotic inactivation;  rifampin;  rifapentine;  rifabutin;  rifampin ADP-ribosyltransferase (Arr);  rifaximin;  rifamycin antibiotic; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
744	UPDATE	vanS gene in vanL cluster	 glycopeptide antibiotic;  vanS;  antibiotic target alteration;  vancomycin;  glycopeptide resistance gene cluster; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with vancomycin
UPDATED category_aro_cvterm_id with 35947
UPDATED category_aro_accession with 0000028
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
745	UPDATE	CMY-40	 antibiotic inactivation;  CMY beta-lactamase;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
746	UPDATE	AAC(2')-Ib	 antibiotic inactivation;  AAC(2');  arbekacin;  gentamicin B;  gentamicin C;  amikacin;  aminoglycoside antibiotic;  tobramycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
747	UPDATE	QnrA4	 sparfloxacin;  norfloxacin;  quinolone resistance protein (qnr);  gatifloxacin;  levofloxacin;  antibiotic target protection;  ciprofloxacin;  fluoroquinolone antibiotic;  nalidixic acid;  moxifloxacin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
748	UPDATE	cmeB	 antibiotic efflux;  resistance-nodulation-cell division (RND) antibiotic efflux pump;  macrolide antibiotic;  cefotaxime;  efflux pump complex or subunit conferring antibiotic resistance;  cephalosporin;  fusidane antibiotic;  fusidic acid;  fluoroquinolone antibiotic;  erythromycin; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_name with fusidane antibiotic
UPDATED category_aro_cvterm_id with 45735
UPDATED category_aro_accession with 3007153
UPDATED category_aro_class_name with Drug Class
UPDATED category_aro_description with A group of antibiotics possessing steroid rings or steroid-like structures.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4811	UPDATE	OXA-114k	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1185	UPDATE	OXA-176	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1799	UPDATE	TEM-147	 penam;  antibiotic inactivation;  penem;  cephalosporin;  monobactam;  ampicillin;  TEM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2913	UPDATE	OXA-286	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
926	UPDATE	KPC-15	 antibiotic inactivation;  penam;  carbapenem;  cephalosporin;  monobactam;  KPC beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1050	UPDATE	AAC(6')-Ii	 AAC(6');  antibiotic inactivation;  aminoglycoside antibiotic;  plazomicin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5356	UPDATE	PDC-219	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5355	UPDATE	PDC-218	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5354	UPDATE	PDC-217	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5353	UPDATE	PDC-216	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5352	UPDATE	PDC-215	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5351	UPDATE	PDC-214	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5350	UPDATE	PDC-213	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1058	UPDATE	VIM-27	 penam;  antibiotic inactivation;  penem;  carbapenem;  cephalosporin;  cephamycin;  VIM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1059	UPDATE	APH(9)-Ib	 antibiotic inactivation;  aminoglycoside antibiotic;  APH(9);  spectinomycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5359	UPDATE	PDC-22	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5358	UPDATE	PDC-21b	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1696	UPDATE	Salmonella serovars gyrB conferring resistance to fluoroquinolones	 fluoroquinolone resistant gyrB;  grepafloxacin;  trovafloxacin;  ofloxacin;  norfloxacin;  nalidixic acid;  lomefloxacin;  gatifloxacin;  levofloxacin;  sparfloxacin;  antibiotic target alteration;  enoxacin;  ciprofloxacin;  pefloxacin;  fluoroquinolone antibiotic;  moxifloxacin; 	model_description; model_param	"UPDATED model_description with Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
"
1697	UPDATE	TEM-135	 penam;  antibiotic inactivation;  penem;  cephalosporin;  penicillin;  monobactam;  ampicillin;  TEM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1694	UPDATE	OXA-353	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1695	UPDATE	DHA-5	 antibiotic inactivation;  cephalosporin;  cephamycin;  DHA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1692	UPDATE	tet(M)	 chlortetracycline;  demeclocycline;  oxytetracycline;  tetracycline antibiotic;  tetracycline;  antibiotic target protection;  minocycline;  tetracycline-resistant ribosomal protection protein;  doxycycline; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1693	UPDATE	TEM-143	 penam;  antibiotic inactivation;  penem;  cephalosporin;  monobactam;  ampicillin;  TEM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1690	UPDATE	OXA-317	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1691	UPDATE	CMY-31	 antibiotic inactivation;  CMY beta-lactamase;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
715	UPDATE	PDC-3	 penam;  carbapenem;  monobactam;  piperacillin-tazobactam;  cephalosporin;  cefazolin;  ampicillin;  ceftazidime;  cefalotin;  cephamycin;  antibiotic inactivation;  cefixime;  amoxicillin;  PDC beta-lactamase;  clavulanic acid;  piperacillin;  tazobactam;  ceftriaxone;  cefoxitin;  amoxicillin-clavulanic acid; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1698	UPDATE	OCH-6	 penam;  antibiotic inactivation;  penem;  cephalosporin;  cephamycin;  monobactam;  OCH beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1699	UPDATE	vanX gene in vanO cluster	 glycopeptide antibiotic;  glycopeptide resistance gene cluster;  vanX;  vancomycin;  antibiotic target alteration; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with vancomycin
UPDATED category_aro_cvterm_id with 35947
UPDATED category_aro_accession with 0000028
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.
UPDATED param_value with 200
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4310	UPDATE	ADC-244	 antibiotic inactivation;  cephalosporin;  ADC beta-lactamases pending classification for carbapenemase activity; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1279	UPDATE	TEM-104	 penam;  antibiotic inactivation;  penem;  cephalosporin;  monobactam;  ampicillin;  TEM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4312	UPDATE	ADC-246	 antibiotic inactivation;  cephalosporin;  ADC beta-lactamases pending classification for carbapenemase activity; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
619	UPDATE	SHV-30	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  SHV beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4314	UPDATE	ADC-248	 antibiotic inactivation;  cephalosporin;  ADC beta-lactamases pending classification for carbapenemase activity; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4817	UPDATE	OXA-114r	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4316	UPDATE	ADC-250	 antibiotic inactivation;  cephalosporin;  ADC beta-lactamases pending classification for carbapenemase activity; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4317	UPDATE	ADC-251	 antibiotic inactivation;  cephalosporin;  ADC beta-lactamases pending classification for carbapenemase activity; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
612	UPDATE	PDC-7	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4319	UPDATE	ADC-253	 antibiotic inactivation;  cephalosporin;  ADC beta-lactamases pending classification for carbapenemase activity; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1272	UPDATE	CTX-M-67	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
611	UPDATE	OXA-328	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
616	UPDATE	NDM-8	 antibiotic inactivation;  penam;  carbapenem;  cephalosporin;  cephamycin;  NDM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1275	UPDATE	ErmT	 streptogramin A antibiotic;  antibiotic target alteration;  virginiamycin S2;  vernamycin C;  pristinamycin IC;  patricin B;  patricin A;  oleandomycin;  ostreogrycin B3;  macrolide antibiotic;  telithromycin;  tylosin;  lincosamide antibiotic;  dirithromycin;  clarithromycin;  clindamycin;  dalfopristin;  pristinamycin IB;  quinupristin;  pristinamycin IA;  Erm 23S ribosomal RNA methyltransferase;  virginiamycin M1;  madumycin II;  griseoviridin;  streptogramin B antibiotic;  lincomycin;  streptogramin antibiotic;  roxithromycin;  spiramycin;  azithromycin;  erythromycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
614	UPDATE	SFB-1	 penam;  antibiotic inactivation;  cephalosporin;  SHW beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1277	UPDATE	GES-16	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  GES beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
711	UPDATE	SHV-62	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  SHV beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
615	UPDATE	OXA-211	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4911	UPDATE	OXA-585	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4429	UPDATE	CARB-45	 penam;  antibiotic inactivation;  CARB beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
710	UPDATE	dfrB6	 trimethoprim;  diaminopyrimidine antibiotic;  trimethoprim resistant dihydrofolate reductase dfr;  antibiotic target replacement; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4380	UPDATE	BlaB-19	 carbapenem;  penam;  antibiotic inactivation;  BlaB beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
331	UPDATE	TEM-166	 penam;  antibiotic inactivation;  penem;  cephalosporin;  monobactam;  ampicillin;  TEM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5279	UPDATE	PDC-142	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3333	UPDATE	ADC-73	 antibiotic inactivation;  cephalosporin;  ADC beta-lactamase without carbapenemase activity; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4816	UPDATE	OXA-114q	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1180	UPDATE	mdsC	 penam;  antibiotic efflux;  resistance-nodulation-cell division (RND) antibiotic efflux pump;  penem;  carbapenem;  efflux pump complex or subunit conferring antibiotic resistance;  cephalosporin;  cephamycin;  monobactam;  phenicol antibiotic;  chloramphenicol; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3332	UPDATE	ADC-67	 antibiotic inactivation;  cephalosporin;  ADC beta-lactamase without carbapenemase activity; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4682	UPDATE	IMP-46	 penam;  antibiotic inactivation;  penem;  carbapenem;  cephalosporin;  IMP beta-lactamase;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4926	UPDATE	OXA-600	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4269	UPDATE	ADC-204	 antibiotic inactivation;  cephalosporin;  ADC beta-lactamases pending classification for carbapenemase activity; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3331	UPDATE	ADC-62	 antibiotic inactivation;  cephalosporin;  ADC beta-lactamase without carbapenemase activity; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2371	UPDATE	ADC-82	 antibiotic inactivation;  cephalosporin;  ADC beta-lactamase without carbapenemase activity; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1472	UPDATE	DHA-18	 antibiotic inactivation;  cephalosporin;  cephamycin;  DHA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1473	UPDATE	CTX-M-44	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1470	UPDATE	QnrB26	 sparfloxacin;  norfloxacin;  quinolone resistance protein (qnr);  gatifloxacin;  levofloxacin;  antibiotic target protection;  ciprofloxacin;  fluoroquinolone antibiotic;  nalidixic acid;  moxifloxacin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3330	UPDATE	Mycoplasma genitalium gyrA mutation confers resistance to fluoroquinolones	 antibiotic target alteration;  fluoroquinolone antibiotic;  moxifloxacin;  fluoroquinolone resistant gyrA; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
UPDATED category_aro_name with moxifloxacin
UPDATED category_aro_cvterm_id with 35991
UPDATED category_aro_accession with 0000074
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
"
1476	UPDATE	TEM-199	 penam;  antibiotic inactivation;  penem;  cephalosporin;  monobactam;  ampicillin;  TEM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1474	UPDATE	MexR	 sulfonamide antibiotic;  penem;  panipenem;  antibiotic target alteration;  tetracycline antibiotic;  clavulanic acid;  meropenem;  antibiotic efflux;  resistance-nodulation-cell division (RND) antibiotic efflux pump;  aztreonam;  trimethoprim;  aminocoumarin antibiotic;  cephalosporin;  macrolide antibiotic;  carbapenem;  ceftazidime;  ciprofloxacin;  cephamycin;  ceftriaxone;  amoxicillin-clavulanic acid;  colistin B;  protein(s) and two-component regulatory system modulating antibiotic efflux;  colistin A;  peptide antibiotic;  diaminopyrimidine antibiotic;  ampicillin;  amoxicillin;  penam;  sulfamethoxazole;  novobiocin;  efflux pump complex or subunit conferring antibiotic resistance;  trimethoprim-sulfamethoxazole;  tetracycline;  monobactam;  fluoroquinolone antibiotic;  erythromycin;  phenicol antibiotic;  azithromycin;  chloramphenicol; 	model_description; model_param	"UPDATED model_description with Protein Overexpression Models (POM) are similar to Protein Variant Models (PVM) in that they include a protein reference sequence, a curated BLASTP bitscore cut-off, and mapped resistance variants. Whereas PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, reporting only those with curated mutations conferring AMR, POMs are restricted to regulatory proteins and report both wild-type sequences and/or sequences with mutations leading to overexpression of efflux complexes. The former lead to efflux of antibiotics at basal levels, while the latter can confer clinical resistance. POMs include a protein reference sequence (often from wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Perfect RGI match is 100% identical to the wild-type reference protein sequence along its entire length, a Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value may or may not contain at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off may or may not contain at least one curated mutation from amongst the mapped resistance variants.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
"
1475	UPDATE	SHV-99	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  SHV beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3337	UPDATE	Corynebacterium striatum tetA	 penam;  antibiotic efflux;  major facilitator superfamily (MFS) antibiotic efflux pump;  oxytetracycline;  efflux pump complex or subunit conferring antibiotic resistance;  oxacillin;  tetracycline antibiotic;  tetracycline; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1478	UPDATE	CARB-10	 penam;  antibiotic inactivation;  CARB beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1479	UPDATE	IMP-40	 penam;  antibiotic inactivation;  penem;  carbapenem;  cephalosporin;  IMP beta-lactamase;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1495	UPDATE	ACT-4	 antibiotic inactivation;  carbapenem;  penam;  ACT beta-lactamase;  cephalosporin;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1304	UPDATE	CTX-M-85	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1305	UPDATE	OprM	 sulfonamide antibiotic;  tetracycline;  erythromycin;  penem;  panipenem;  thiamphenicol;  tetracycline antibiotic;  clavulanic acid;  meropenem;  antibiotic efflux;  resistance-nodulation-cell division (RND) antibiotic efflux pump;  aztreonam;  ofloxacin;  norfloxacin;  trimethoprim;  aminocoumarin antibiotic;  cephalosporin;  macrolide antibiotic;  carbapenem;  ceftazidime;  ciprofloxacin;  cephamycin;  gentamicin C;  amikacin;  ceftriaxone;  disinfecting agents and antiseptics;  amoxicillin-clavulanic acid;  colistin B;  colistin A;  peptide antibiotic;  diaminopyrimidine antibiotic;  ticarcillin;  ampicillin;  amoxicillin;  penam;  aminoglycoside antibiotic;  sulfamethoxazole;  novobiocin;  phenicol antibiotic;  efflux pump complex or subunit conferring antibiotic resistance;  trimethoprim-sulfamethoxazole;  acriflavine;  monobactam;  fluoroquinolone antibiotic;  chloramphenicol;  nalidixic acid;  azithromycin;  tobramycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1306	UPDATE	IND-5	 carbapenem;  antibiotic inactivation;  IND beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1307	UPDATE	OXY-1-6	 penam;  OXY beta-lactamase;  cephalosporin;  antibiotic inactivation;  monobactam; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1300	UPDATE	MexF	 antibiotic efflux;  resistance-nodulation-cell division (RND) antibiotic efflux pump;  norfloxacin;  trimethoprim;  efflux pump complex or subunit conferring antibiotic resistance;  diaminopyrimidine antibiotic;  ciprofloxacin;  fluoroquinolone antibiotic;  phenicol antibiotic;  chloramphenicol; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1301	UPDATE	Staphylococcus aureus cls conferring resistance to daptomycin	 peptide antibiotic;  antibiotic target alteration;  daptomycin resistant cls;  daptomycin; 	model_description; model_param	"UPDATED model_description with Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
"
4469	UPDATE	CMY-106	 antibiotic inactivation;  CMY beta-lactamase;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1303	UPDATE	BEL-2	 penam;  monobactam;  cephalosporin;  antibiotic inactivation;  BEL beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3334	UPDATE	AAC(6')-Il	 antibiotic inactivation;  AAC(6');  kanamycin A;  amikacin;  aminoglycoside antibiotic;  tobramycin; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with kanamycin A
UPDATED category_aro_cvterm_id with 35966
UPDATED category_aro_accession with 0000049
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.
UPDATED category_aro_name with amikacin
UPDATED category_aro_cvterm_id with 35932
UPDATED category_aro_accession with 0000013
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.
UPDATED category_aro_name with tobramycin
UPDATED category_aro_cvterm_id with 35969
UPDATED category_aro_accession with 0000052
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1308	UPDATE	vanT gene in vanE cluster	 glycopeptide antibiotic;  glycopeptide resistance gene cluster;  antibiotic target alteration;  vancomycin;  vanT; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with vancomycin
UPDATED category_aro_cvterm_id with 35947
UPDATED category_aro_accession with 0000028
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.
UPDATED param_value with 200
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1309	UPDATE	ACT-20	 antibiotic inactivation;  carbapenem;  penam;  ACT beta-lactamase;  cephalosporin;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5740	UPDATE	salE	 retapamulin;  sal-type ABC-F protein;  pleuromutilin antibiotic;  tiamulin;  streptogramin A antibiotic;  antibiotic target protection;  streptogramin antibiotic;  lincosamide antibiotic; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5469	UPDATE	PDC-34	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5742	UPDATE	Erm(52)	 Erm 23S ribosomal RNA methyltransferase;  macrolide antibiotic;  antibiotic target alteration;  streptogramin antibiotic;  clindamycin;  lincosamide antibiotic; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with clindamycin
UPDATED category_aro_cvterm_id with 35983
UPDATED category_aro_accession with 0000066
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Clindamycin is a lincosamide antibiotic that blocks A-site aminoacyl-tRNA binding. It is usually used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5743	UPDATE	msr(G)	 macrolide antibiotic;  msr-type ABC-F protein;  antibiotic target protection;  streptogramin antibiotic;  azithromycin;  erythromycin; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with azithromycin
UPDATED category_aro_cvterm_id with 36297
UPDATED category_aro_accession with 3000158
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Azithromycin is a 15-membered macrolide and falls under the subclass of azalide. Like other macrolides, azithromycin binds bacterial ribosomes to inhibit protein synthesis. The nitrogen substitution at the C-9a position prevents its degradation.
UPDATED category_aro_name with erythromycin
UPDATED category_aro_cvterm_id with 35925
UPDATED category_aro_accession with 0000006
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure/function processes critical for life or replication are inhibited.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
498	UPDATE	QnrB17	 sparfloxacin;  norfloxacin;  quinolone resistance protein (qnr);  gatifloxacin;  levofloxacin;  antibiotic target protection;  ciprofloxacin;  fluoroquinolone antibiotic;  nalidixic acid;  moxifloxacin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5745	UPDATE	mefF	 efflux pump complex or subunit conferring antibiotic resistance;  major facilitator superfamily (MFS) antibiotic efflux pump;  macrolide antibiotic;  antibiotic efflux; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5746	UPDATE	Erm(51)	 pristinamycin IB;  Erm 23S ribosomal RNA methyltransferase;  macrolide antibiotic;  streptogramin B antibiotic;  streptogramin antibiotic;  antibiotic target alteration;  lincosamide antibiotic;  clarithromycin;  clindamycin;  azithromycin;  erythromycin; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with pristinamycin IB
UPDATED category_aro_cvterm_id with 37019
UPDATED category_aro_accession with 3000675
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Pristinamycin IB is a class B streptogramin similar to pristinamycin IA, the former containing a N-methyl-4-(methylamino)phenylalanine instead of a N-methyl-4-(dimethylamino)phenylalanine in its class A streptogramin counterpart (one less methyl group).
UPDATED category_aro_name with streptogramin B antibiotic
UPDATED category_aro_cvterm_id with 35967
UPDATED category_aro_accession with 0000050
UPDATED category_aro_class_name with Drug Class
UPDATED category_aro_description with Streptogramin B antibiotics are are cyclic hepta- or hexa-depsipeptides.  Type B streptogramins block the peptide exit tunnel of the 50S bacterial ribosome. The general composition of group B streptogramins is 3-hydroxypicolinic acid-L-Thr-D-aminobutyric acid (or D-Ala)-L-Pro-L-Phe (or 4-N-,N-(dimethylamino)-L-Phe)-X-L-phenylglycine. Used alone, streptogramin B antibiotics are bacteriostatic, but is bactericidal when used with streptogramin A antibiotics.
UPDATED category_aro_name with clarithromycin
UPDATED category_aro_cvterm_id with 35982
UPDATED category_aro_accession with 0000065
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Clarithromycin is a methyl derivative of erythromycin, sharing the 14-carbon macrolide ring. The antibiotic binds to the 50S subunit of the ribosome and is used to treat pharyngitis, tonsillitis, acute maxillary sinusitis, acute bacterial exacerbation of chronic bronchitis, pneumonia (especially atypical pneumonias associated with Chlamydia pneumoniae or TWAR), and skin structure infections.
UPDATED category_aro_name with clindamycin
UPDATED category_aro_cvterm_id with 35983
UPDATED category_aro_accession with 0000066
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Clindamycin is a lincosamide antibiotic that blocks A-site aminoacyl-tRNA binding. It is usually used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria.
UPDATED category_aro_name with azithromycin
UPDATED category_aro_cvterm_id with 36297
UPDATED category_aro_accession with 3000158
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Azithromycin is a 15-membered macrolide and falls under the subclass of azalide. Like other macrolides, azithromycin binds bacterial ribosomes to inhibit protein synthesis. The nitrogen substitution at the C-9a position prevents its degradation.
UPDATED category_aro_name with erythromycin
UPDATED category_aro_cvterm_id with 35925
UPDATED category_aro_accession with 0000006
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure/function processes critical for life or replication are inhibited.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5747	UPDATE	mefH	 efflux pump complex or subunit conferring antibiotic resistance;  major facilitator superfamily (MFS) antibiotic efflux pump;  macrolide antibiotic;  antibiotic efflux; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
494	UPDATE	KPC-14	 antibiotic inactivation;  penam;  carbapenem;  cephalosporin;  monobactam;  KPC beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5749	UPDATE	mreA	 efflux pump complex or subunit conferring antibiotic resistance;  major facilitator superfamily (MFS) antibiotic efflux pump;  macrolide antibiotic;  antibiotic efflux; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4226	UPDATE	ADC-156	 antibiotic inactivation;  cephalosporin;  ADC beta-lactamases pending classification for carbapenemase activity; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
497	UPDATE	OXA-79	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4220	UPDATE	ADC-150	 antibiotic inactivation;  cephalosporin;  ADC beta-lactamases pending classification for carbapenemase activity; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4221	UPDATE	ADC-151	 antibiotic inactivation;  cephalosporin;  ADC beta-lactamases pending classification for carbapenemase activity; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4222	UPDATE	ADC-152	 antibiotic inactivation;  cephalosporin;  ADC beta-lactamases pending classification for carbapenemase activity; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4223	UPDATE	ADC-153	 antibiotic inactivation;  cephalosporin;  ADC beta-lactamases pending classification for carbapenemase activity; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5586	UPDATE	PDC-459	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5587	UPDATE	PDC-46	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5584	UPDATE	PDC-457	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5585	UPDATE	PDC-458	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
20	UPDATE	CMY-1	 antibiotic inactivation;  CMY beta-lactamase;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
21	UPDATE	OXA-329	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5580	UPDATE	PDC-453	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
23	UPDATE	OXA-371	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
927	UPDATE	OXA-381	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
28	UPDATE	OXA-45	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
29	UPDATE	Escherichia coli folP with mutation conferring resistance to sulfonamides	 sulfadiazine;  sulfadoxine;  sulfacetamide;  sulfadimidine;  mafenide;  sulfonamide resistant dihydropteroate synthase folP;  sulfisoxazole;  antibiotic target alteration;  sulfamethizole;  sulfasalazine;  sulfamethoxazole;  sulfonamide antibiotic; 	model_description; model_param	"UPDATED model_description with Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
"
5588	UPDATE	PDC-460	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5589	UPDATE	PDC-462	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4311	UPDATE	ADC-245	 antibiotic inactivation;  cephalosporin;  ADC beta-lactamases pending classification for carbapenemase activity; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
901	UPDATE	LCR-1	 LCR beta-lactamase;  penam;  cephalosporin;  antibiotic inactivation; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3262	UPDATE	dfrA29	 trimethoprim;  diaminopyrimidine antibiotic;  trimethoprim resistant dihydrofolate reductase dfr;  antibiotic target replacement; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4876	UPDATE	OXA-547	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3599	UPDATE	GOB-13	 carbapenem;  penam;  GOB beta-lactamase;  antibiotic inactivation;  cephalosporin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5267	UPDATE	PDC-130	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3598	UPDATE	GOB-12	 carbapenem;  penam;  GOB beta-lactamase;  antibiotic inactivation;  cephalosporin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3939	UPDATE	CMY-153	 antibiotic inactivation;  CMY beta-lactamase;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3938	UPDATE	CMY-89	 antibiotic inactivation;  CMY beta-lactamase;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5266	UPDATE	PDC-13	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3935	UPDATE	CMY-128	 antibiotic inactivation;  CMY beta-lactamase;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3934	UPDATE	CMY-151	 antibiotic inactivation;  CMY beta-lactamase;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3937	UPDATE	CMY-127	 antibiotic inactivation;  CMY beta-lactamase;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3936	UPDATE	CMY-129	 antibiotic inactivation;  CMY beta-lactamase;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3931	UPDATE	CMY-121	 antibiotic inactivation;  CMY beta-lactamase;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3930	UPDATE	SHV-216	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  SHV beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3933	UPDATE	CMY-97	 antibiotic inactivation;  CMY beta-lactamase;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3932	UPDATE	CMY-152	 antibiotic inactivation;  CMY beta-lactamase;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1703	UPDATE	FosK	 antibiotic inactivation;  fosfomycin thiol transferase;  phosphonic acid antibiotic; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
DELETED 35944
UPDATED category_aro_name with phosphonic acid antibiotic
UPDATED category_aro_cvterm_id with 45731
UPDATED category_aro_accession with 3007149
UPDATED category_aro_class_name with Drug Class
UPDATED category_aro_description with A group of antibiotics derived from phosphonic acids.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5263	UPDATE	PDC-127	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1516	UPDATE	CMY-45	 antibiotic inactivation;  CMY beta-lactamase;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5262	UPDATE	PDC-126	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4138	UPDATE	ACT-47	 antibiotic inactivation;  carbapenem;  penam;  ACT beta-lactamase;  cephalosporin;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4139	UPDATE	ACT-48	 antibiotic inactivation;  carbapenem;  penam;  ACT beta-lactamase;  cephalosporin;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5261	UPDATE	PDC-125	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1877	UPDATE	CMY-12	 antibiotic inactivation;  CMY beta-lactamase;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4130	UPDATE	ACT-39	 antibiotic inactivation;  carbapenem;  penam;  ACT beta-lactamase;  cephalosporin;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4131	UPDATE	ACT-40	 antibiotic inactivation;  carbapenem;  penam;  ACT beta-lactamase;  cephalosporin;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4132	UPDATE	ACT-41	 antibiotic inactivation;  carbapenem;  penam;  ACT beta-lactamase;  cephalosporin;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4133	UPDATE	ACT-42	 antibiotic inactivation;  carbapenem;  penam;  ACT beta-lactamase;  cephalosporin;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4134	UPDATE	ACT-43	 antibiotic inactivation;  carbapenem;  penam;  ACT beta-lactamase;  cephalosporin;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4135	UPDATE	ACT-44	 antibiotic inactivation;  carbapenem;  penam;  ACT beta-lactamase;  cephalosporin;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4136	UPDATE	ACT-45	 antibiotic inactivation;  carbapenem;  penam;  ACT beta-lactamase;  cephalosporin;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4137	UPDATE	ACT-46	 antibiotic inactivation;  carbapenem;  penam;  ACT beta-lactamase;  cephalosporin;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5692	UPDATE	VIM-41	 penam;  antibiotic inactivation;  penem;  carbapenem;  cephalosporin;  cephamycin;  VIM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5693	UPDATE	VIM-44	 penam;  antibiotic inactivation;  penem;  carbapenem;  cephalosporin;  cephamycin;  VIM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5690	UPDATE	VHW-1	 carbapenem;  antibiotic inactivation;  cephalosporin;  VHW beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5691	UPDATE	VIM-40	 penam;  antibiotic inactivation;  penem;  carbapenem;  cephalosporin;  cephamycin;  VIM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5696	UPDATE	VIM-47	 penam;  antibiotic inactivation;  penem;  carbapenem;  cephalosporin;  cephamycin;  VIM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5697	UPDATE	VIM-48	 penam;  antibiotic inactivation;  penem;  carbapenem;  cephalosporin;  cephamycin;  VIM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3847	UPDATE	lsaD	 virginiamycin M1;  pleuromutilin antibiotic;  lsa-type ABC-F protein;  tiamulin;  streptogramin A antibiotic;  lincomycin;  antibiotic target protection;  streptogramin antibiotic;  clindamycin;  lincosamide antibiotic; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with streptogramin A antibiotic
UPDATED category_aro_cvterm_id with 35952
UPDATED category_aro_accession with 0000034
UPDATED category_aro_class_name with Drug Class
UPDATED category_aro_description with Streptogramin A antibiotics are cyclic polyketide peptide hybrids that bind to the ribosomal peptidyl transfer centre. Structural variation arises from substituting a proline for its desaturated derivative and by its substitution for Ala or Cys. Used alone, streptogramin A antibiotics are bacteriostatic, but is bactericidal when used with streptogramin B antibiotics.
UPDATED category_aro_name with lincomycin
UPDATED category_aro_cvterm_id with 35964
UPDATED category_aro_accession with 0000046
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Lincomycin is a lincosamide antibiotic that comes from the actinomyces Streptomyces lincolnensis. It binds to the 23s portion of the 50S subunit of bacterial ribosomes and inhibit early elongation of peptide chain by inhibiting transpeptidase reaction.
UPDATED category_aro_name with virginiamycin M1
UPDATED category_aro_cvterm_id with 37013
UPDATED category_aro_accession with 3000669
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Virginiamycin M1 is a streptogramin A antibiotic.
UPDATED category_aro_name with tiamulin
UPDATED category_aro_cvterm_id with 37015
UPDATED category_aro_accession with 3000671
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Tiamulin is a pleuromutilin derivative currently used in veterinary medicine. It binds to the 23 rRNA of the 50S ribosomal subunit to inhibit protein translation.
UPDATED category_aro_name with clindamycin
UPDATED category_aro_cvterm_id with 35983
UPDATED category_aro_accession with 0000066
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Clindamycin is a lincosamide antibiotic that blocks A-site aminoacyl-tRNA binding. It is usually used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3846	UPDATE	AAC(6')-Ib-cr9	 antibiotic inactivation;  AAC(6')-Ib-cr;  kanamycin A;  ciprofloxacin;  fluoroquinolone antibiotic;  amikacin;  aminoglycoside antibiotic;  tobramycin; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with kanamycin A
UPDATED category_aro_cvterm_id with 35966
UPDATED category_aro_accession with 0000049
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.
UPDATED category_aro_name with amikacin
UPDATED category_aro_cvterm_id with 35932
UPDATED category_aro_accession with 0000013
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.
UPDATED category_aro_name with tobramycin
UPDATED category_aro_cvterm_id with 35969
UPDATED category_aro_accession with 0000052
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.
UPDATED category_aro_name with ciprofloxacin
UPDATED category_aro_cvterm_id with 35954
UPDATED category_aro_accession with 0000036
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3849	UPDATE	PDC-70	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3848	UPDATE	PDC-68	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5698	UPDATE	VIM-49	 penam;  antibiotic inactivation;  penem;  carbapenem;  cephalosporin;  cephamycin;  VIM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5699	UPDATE	VIM-50	 penam;  antibiotic inactivation;  penem;  carbapenem;  cephalosporin;  cephamycin;  VIM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4875	UPDATE	OXA-546	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1063	UPDATE	QnrB73	 sparfloxacin;  norfloxacin;  quinolone resistance protein (qnr);  gatifloxacin;  levofloxacin;  antibiotic target protection;  ciprofloxacin;  fluoroquinolone antibiotic;  nalidixic acid;  moxifloxacin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4465	UPDATE	CMH-3	 antibiotic inactivation;  CMH beta-lactamase;  cephalosporin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1873	UPDATE	linG	 antibiotic inactivation;  lincosamide nucleotidyltransferase (LNU);  lincomycin;  lincosamide antibiotic; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED category_aro_name with lincomycin
UPDATED category_aro_cvterm_id with 35964
UPDATED category_aro_accession with 0000046
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Lincomycin is a lincosamide antibiotic that comes from the actinomyces Streptomyces lincolnensis. It binds to the 23s portion of the 50S subunit of bacterial ribosomes and inhibit early elongation of peptide chain by inhibiting transpeptidase reaction.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2136	UPDATE	Escherichia coli 16S rRNA (rrsB) mutation conferring resistance to kanamycin A	 kanamycin A;  antibiotic target alteration;  aminoglycoside antibiotic;  16s rRNA with mutation conferring resistance to aminoglycoside antibiotics; 	model_description; model_param	"UPDATED model_description with Ribosomal RNA (rRNA) Gene Variant Models (RVM) are similar to Protein Variant Models (PVM), i.e. detect  sequences based on their similarity to a curated reference sequence and secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles, except RVMs are designed to detect AMR acquired via mutation of genes encoding ribosomal RNAs (rRNA). RVMs include a rRNA reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTN bit-score above the curated BLASTN cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTN bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
UPDATED param_description with The BLASTN bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
"
1870	UPDATE	OXA-66	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3916	UPDATE	CMY-122	 antibiotic inactivation;  CMY beta-lactamase;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1065	UPDATE	OXA-384	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1871	UPDATE	OXA-389	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5793	UPDATE	tet(O/W/O)	 tetracycline antibiotic;  tetracycline-resistant ribosomal protection protein;  antibiotic target protection;  tetracycline; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1064	UPDATE	CTX-M-141	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
1067	UPDATE	MexE	 antibiotic efflux;  resistance-nodulation-cell division (RND) antibiotic efflux pump;  norfloxacin;  trimethoprim;  efflux pump complex or subunit conferring antibiotic resistance;  diaminopyrimidine antibiotic;  ciprofloxacin;  fluoroquinolone antibiotic;  phenicol antibiotic;  chloramphenicol; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5268	UPDATE	PDC-131	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
301	UPDATE	CMY-95	 antibiotic inactivation;  CMY beta-lactamase;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4044	UPDATE	PDC-429	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4045	UPDATE	PDC-449	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4046	UPDATE	OXA-540	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4047	UPDATE	OXA-779	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4040	UPDATE	PDC-393	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4041	UPDATE	PDC-119	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4042	UPDATE	PDC-313	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4043	UPDATE	PDC-257	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4315	UPDATE	ADC-249	 antibiotic inactivation;  cephalosporin;  ADC beta-lactamases pending classification for carbapenemase activity; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3910	UPDATE	CMY-154	 antibiotic inactivation;  CMY beta-lactamase;  cephamycin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4048	UPDATE	OXA-838	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4049	UPDATE	OXA-539	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4438	UPDATE	CARB-54	 penam;  antibiotic inactivation;  CARB beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
447	UPDATE	SHV-67	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  SHV beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
7	UPDATE	CTX-M-130	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2288	UPDATE	Mycobacterium tuberculosis variant bovis ndh with mutation conferring resistance to isoniazid	 isoniazid;  antibiotic target alteration;  isoniazid-like antibiotic;  antibiotic resistant ndh; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_name with isoniazid-like antibiotic
UPDATED category_aro_cvterm_id with 45734
UPDATED category_aro_accession with 3007152
UPDATED category_aro_class_name with Drug Class
UPDATED category_aro_description with A group of antibiotics containing isoniazid and its derivatives.
UPDATED param_description with A subtype of the insertion mutation detection model parameter used when a set of insertion mutations are reported in a nucleotide sequence format, encoded as [+]nt[position]:[nucleotides], for example +nt391:GG. Such mutations may be of variable length, possibly causing a frameshift but not causing premature termination or a functional knockout.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
"
3664	UPDATE	NDM-23	 antibiotic inactivation;  penam;  carbapenem;  cephalosporin;  cephamycin;  NDM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3666	UPDATE	NDM-25	 antibiotic inactivation;  penam;  carbapenem;  cephalosporin;  cephamycin;  NDM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3661	UPDATE	NDM-20	 antibiotic inactivation;  penam;  carbapenem;  cephalosporin;  cephamycin;  NDM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3660	UPDATE	NDM-19	 antibiotic inactivation;  penam;  carbapenem;  cephalosporin;  cephamycin;  NDM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3663	UPDATE	NDM-22	 antibiotic inactivation;  penam;  carbapenem;  cephalosporin;  cephamycin;  NDM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
3662	UPDATE	NDM-21	 antibiotic inactivation;  penam;  carbapenem;  cephalosporin;  cephamycin;  NDM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2281	UPDATE	Brucella suis mprF	 peptide antibiotic;  antibiotic target alteration;  defensin resistant mprF;  defensin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2282	UPDATE	Clostridium perfringens mprF	 peptide antibiotic;  antibiotic target alteration;  defensin resistant mprF;  defensin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2283	UPDATE	Streptococcus agalactiae mprF	 peptide antibiotic;  antibiotic target alteration;  defensin resistant mprF;  defensin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2284	UPDATE	Escherichia coli murA with mutation conferring resistance to fosfomycin	 antibiotic target alteration;  phosphonic acid antibiotic;  antibiotic-resistant murA transferase; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
DELETED 35944
UPDATED category_aro_name with phosphonic acid antibiotic
UPDATED category_aro_cvterm_id with 45731
UPDATED category_aro_accession with 3007149
UPDATED category_aro_class_name with Drug Class
UPDATED category_aro_description with A group of antibiotics derived from phosphonic acids.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
"
3668	UPDATE	NDM-27	 antibiotic inactivation;  penam;  carbapenem;  cephalosporin;  cephamycin;  NDM beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2286	UPDATE	Borreliella burgdorferi murA with mutation conferring resistance to fosfomycin	 antibiotic target alteration;  phosphonic acid antibiotic;  antibiotic-resistant murA transferase; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
DELETED 35944
UPDATED category_aro_name with phosphonic acid antibiotic
UPDATED category_aro_cvterm_id with 45731
UPDATED category_aro_accession with 3007149
UPDATED category_aro_class_name with Drug Class
UPDATED category_aro_description with A group of antibiotics derived from phosphonic acids.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
"
2287	UPDATE	Mycolicibacterium smegmatis ndh with mutation conferring resistance to isoniazid	 isoniazid;  antibiotic target alteration;  isoniazid-like antibiotic;  antibiotic resistant ndh; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_name with isoniazid-like antibiotic
UPDATED category_aro_cvterm_id with 45734
UPDATED category_aro_accession with 3007152
UPDATED category_aro_class_name with Drug Class
UPDATED category_aro_description with A group of antibiotics containing isoniazid and its derivatives.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
"
4549	UPDATE	CTX-M-220	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4548	UPDATE	CTX-M-219	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
446	UPDATE	catB8	 antibiotic inactivation;  thiamphenicol;  chloramphenicol acetyltransferase (CAT);  azidamfenicol;  phenicol antibiotic;  chloramphenicol; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
974	UPDATE	lmrC	 celesticetin;  Miscellaneous ABC-F subfamily ATP-binding cassette ribosomal protection proteins;  lincomycin;  antibiotic target protection;  clindamycin;  lincosamide antibiotic; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4541	UPDATE	CTX-M-212	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4540	UPDATE	CTX-M-211	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4543	UPDATE	CTX-M-214	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4542	UPDATE	CTX-M-213	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4545	UPDATE	CTX-M-216	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4544	UPDATE	CTX-M-215	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4547	UPDATE	CTX-M-218	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4546	UPDATE	CTX-M-217	 antibiotic inactivation;  cephalosporin;  CTX-M beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
4828	UPDATE	OXA-396	 carbapenem;  penam;  cephalosporin;  antibiotic inactivation;  OXA beta-lactamase; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2762	UPDATE	MexMN-OprM	 antibiotic efflux;  thiamphenicol;  resistance-nodulation-cell division (RND) antibiotic efflux pump;  efflux pump complex or subunit conferring antibiotic resistance;  phenicol antibiotic;  chloramphenicol; 	model_description; model_param	"UPDATED model_description with Efflux Pump System Meta-Models (EPS) are dedicated to efflux complexes and their regulators, such as AcrAB-TolC. Using the efflux pump components parameter, this model type simply includes a list of detection models for each component of the complex. This model type is still under development and not currently supported by the Resistance Gene Identifier (RGI) software.
UPDATED param_description with Association of proteins within efflux protein complexes or regulatory networks are encoded by the efflux pump components parameter: model_id,model_id,model_id, etc.
"
3268	UPDATE	Clostridioides difficile gyrB conferring resistance to fluoroquinolones	 gemifloxacin;  fluoroquinolone resistant gyrB;  levofloxacin;  ciprofloxacin;  antibiotic target alteration;  fluoroquinolone antibiotic;  moxifloxacin; 	model_description; ARO_category; model_param	"UPDATED model_description with Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
UPDATED category_aro_name with levofloxacin
UPDATED category_aro_cvterm_id with 35988
UPDATED category_aro_accession with 0000071
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.
UPDATED category_aro_name with gemifloxacin
UPDATED category_aro_cvterm_id with 45747
UPDATED category_aro_accession with 3007165
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Gemifloxacin is a broad-spectrum, fourth generation, oral fluoroquinolone antibiotic used in the treatment of various bacterial infections, primarily in the lungs. It has been discontinued for therapeutic use in the US over concerns of tendon and peripheral neuron toxicity, although it is still available for experimental application and elsewhere for therapeutic use. It is usually administered as a mesylate salt, gemifloxacin mesylate.
UPDATED category_aro_name with moxifloxacin
UPDATED category_aro_cvterm_id with 35991
UPDATED category_aro_accession with 0000074
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.
UPDATED category_aro_name with ciprofloxacin
UPDATED category_aro_cvterm_id with 35954
UPDATED category_aro_accession with 0000036
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_description with Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
UPDATED param_description with A nucleotide or amino acid substitution that confers elevated resistance to antibiotic(s) relative to wild type with with format [wild-type][position][mutation], e.g. R184Q.
"
2056	UPDATE	mdtO	 antibiotic efflux;  major facilitator superfamily (MFS) antibiotic efflux pump;  efflux pump complex or subunit conferring antibiotic resistance;  puromycin;  acriflavine;  nucleoside antibiotic;  disinfecting agents and antiseptics; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
5583	UPDATE	PDC-456	 PDC beta-lactamase;  monobactam;  cephalosporin;  antibiotic inactivation;  carbapenem; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2059	UPDATE	OKP-A-1	 penam;  antibiotic inactivation;  OKP beta-lactamase;  cephalosporin; 	model_description; model_param	"UPDATED model_description with Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
UPDATED param_description with The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).
"
2378	UPDATE	Escherichia coli cyaA with mutation conferring resistance to fosfomycin	 antibiotic-resistant cya adenylate cyclase;  fosfomycin;  antibiotic target alteration;  phosphonic acid antibiotic; 	model_description; ARO_category	"UPDATED model_description with Protein Knockout Models (PKM) reflect resistance by the absence of a gene product, most often deletion of a gene involved in antibiotic import, such as Vibrio cholerae OmpT. Like Protein Homolog Models (PHMs), PKMs include a reference sequence and a bitscore cut-off for detection using BLASTP but instead are designed to only report lack of detection under Perfect or Strict criteria. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff. This model type is still under development and not currently supported by the Resistance Gene Identifier (RGI) software.
UPDATED category_aro_class_name with Antibiotic
UPDATED category_aro_name with phosphonic acid antibiotic
UPDATED category_aro_cvterm_id with 45731
UPDATED category_aro_accession with 3007149
UPDATED category_aro_class_name with Drug Class
UPDATED category_aro_description with A group of antibiotics derived from phosphonic acids.
"
2379	UPDATE	Escherichia coli cyaA with mutation conferring resistance to fosfomycin	 antibiotic-resistant cya adenylate cyclase;  fosfomycin;  antibiotic target alteration;  phosphonic acid antibiotic; 	model_description; ARO_category; model_param	"UPDATED