{"$insert": {"8560": {"model_id": "8560", "model_name": "OXA-1054", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"11413": {"protein_sequence": {"accession": "XJP49384.1", "sequence": "MKHIFFVFLILYSNFALAEDKAISALFTAEGVQGTIILKSLRGDKTITHNDARASSRFTSASTFKIFNTLIAVQENVVSLAGTTFKWNGKTYDFPDWNRDQTLESAFKFSCVWCYQEIAKQVGEETYRRYLTLARYGVLTNVADTTTFWLDGSFTVSAVEQIALLEKIYLRELPFRDEAYDALKQVMLAEQTDSYKLYAKTGWAARMNPQIGWYVGYVETSDDVWFFAINLTLRSELDLGLRQKITKAALRAERIIP"}, "dna_sequence": {"accession": "PQ507915.1", "fmin": "0", "fmax": "774", "strand": "+", "sequence": "ATGAAGCATATATTTTTTGTTTTTCTGATTCTGTACTCAAACTTTGCTCTCGCTGAGGATAAAGCGATTTCGGCCCTTTTTACCGCAGAAGGTGTTCAAGGAACCATCATTTTGAAGTCGTTGCGTGGGGATAAGACAATCACGCACAACGATGCACGCGCTTCTAGCCGGTTCACATCAGCCTCGACGTTCAAGATATTCAACACGTTGATTGCTGTTCAAGAAAACGTGGTGAGTTTGGCGGGCACGACATTCAAATGGAATGGAAAAACGTATGATTTCCCCGATTGGAACCGTGACCAAACACTTGAAAGCGCATTCAAATTCTCTTGCGTGTGGTGCTATCAGGAAATCGCCAAGCAAGTGGGGGAAGAAACCTATCGCCGCTACCTTACGCTTGCGAGGTATGGTGTTCTGACCAACGTAGCCGACACTACAACCTTTTGGCTTGATGGCAGCTTTACGGTCAGCGCCGTCGAGCAGATTGCTCTGTTGGAAAAGATCTATCTGCGAGAACTTCCGTTCCGTGATGAAGCCTACGACGCTTTAAAGCAGGTAATGCTGGCAGAGCAGACCGACAGCTACAAACTTTACGCAAAGACTGGCTGGGCAGCAAGGATGAACCCCCAAATTGGGTGGTACGTTGGATATGTTGAAACATCCGATGACGTATGGTTTTTTGCCATCAATTTGACCTTGAGGTCGGAACTTGACTTAGGTTTGCGCCAGAAAATAACAAAGGCTGCGCTTAGGGCTGAACGCATTATTCCCTGA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "36752", "NCBI_taxonomy_name": "Pseudomonas aeruginosa", "NCBI_taxonomy_id": "287"}}}}, "ARO_accession": "3009648", "ARO_id": "48519", "ARO_name": "OXA-1054", "CARD_short_name": "OXA-1054", "ARO_description": "OXA-1054 is an OXA-372-like carabapenem-hydrolzing class D beta-lactamase identified from Pseudomonas aeruginosa.", "ARO_category": {"46506": {"category_aro_accession": "3007717", "category_aro_cvterm_id": "46506", "category_aro_name": "OXA-372-like beta-lactamase", "category_aro_description": "A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-372.", "category_aro_class_name": "AMR Gene Family"}, "35939": {"category_aro_accession": "0000020", "category_aro_cvterm_id": "35939", "category_aro_name": "carbapenem", "category_aro_description": "Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem 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.", "category_aro_class_name": "Drug Class"}, "36017": {"category_aro_accession": "3000008", "category_aro_cvterm_id": "36017", "category_aro_name": "penicillin beta-lactam", "category_aro_description": "Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like 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.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "8563": {"model_id": "8563", "model_name": "AAC(6')-Va", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "275"}}, "model_sequences": {"sequence": {"11415": {"protein_sequence": {"accession": "WKN80832.1", "sequence": "MTNADWRIVPLDETLLAQWATLRQQLWPNHALSAHLQEGAELLAAAHLNAFLVLDAQSQAVAFADAALRRDYVNGCESSPVVYLEGVYVQPASRRRGLAQALIARVAQWGRELGCRELASDAAIDNLASQQLHQRLGFAETERVVFFKKALG"}, "dna_sequence": {"accession": "OQ685298.1", "fmin": "0", "fmax": "459", "strand": "+", "sequence": "ATGACGAACGCCGACTGGCGGATAGTGCCCCTCGACGAGACGCTGCTGGCGCAGTGGGCAACCCTGCGCCAGCAGCTGTGGCCAAACCACGCACTATCGGCACATCTGCAGGAAGGGGCCGAGCTGCTGGCCGCTGCCCATCTCAACGCCTTTCTGGTGCTGGATGCGCAGAGCCAGGCGGTCGCCTTTGCCGATGCCGCCCTGCGCCGCGATTACGTGAACGGCTGCGAGAGCAGCCCTGTGGTCTATCTGGAAGGGGTCTATGTGCAGCCGGCTTCACGCCGGCGCGGGTTGGCCCAGGCCTTGATCGCCCGGGTGGCCCAGTGGGGCCGCGAGCTGGGTTGTCGCGAGCTGGCCTCCGATGCCGCCATCGACAACCTCGCCTCCCAGCAGTTGCACCAGCGACTCGGCTTTGCCGAAACAGAGCGGGTCGTCTTCTTCAAAAAGGCCCTCGGCTGA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "36810", "NCBI_taxonomy_name": "Aeromonas hydrophila", "NCBI_taxonomy_id": "644"}}}}, "ARO_accession": "3009655", "ARO_id": "48526", "ARO_name": "AAC(6')-Va", "CARD_short_name": "AAC(6')-Va", "ARO_description": "AAC(6')-Va is an aminoglycoside modifying enzyme identified from Aeromonas hydrophila, and associated with decreased susceptibility to aminoglycoside antibiotics including ribostamycin.", "ARO_category": {"36484": {"category_aro_accession": "3000345", "category_aro_cvterm_id": "36484", "category_aro_name": "AAC(6')", "category_aro_description": "A category of aminoglycoside N-acetyltransferase enzymes with modification regiospecificity based at the 6'-amino group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics through acetylation of the 6-amino group of the compound.", "category_aro_class_name": "AMR Gene Family"}, "35935": {"category_aro_accession": "0000016", "category_aro_cvterm_id": "35935", "category_aro_name": "aminoglycoside antibiotic", "category_aro_description": "Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "8562": {"model_id": "8562", "model_name": "MrmA", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "600"}}, "model_sequences": {"sequence": {"11414": {"protein_sequence": {"accession": "XQH09930.1", "sequence": "MKRLPKYTPAEVRNDPYGFTYKEMSEVIGENEAKALYEELYKQLPRKKNLSMLVKNICKSSDTEKYVYELKDNKYIETVFIKRRDGGTVCVSTQVGCPVGCIFCESGRNGFVRNLTSSEIVQQIILLRRKVNRIVFMGMGEPLFNYDNLIKAIHILRDRYGLNFPTDGITISTVGPVDQLKKLREEHLKIQLTISLHAATQSARNRIIPHMRIYAIEDVVKQALSYSERHNRKIVFAYLLLPGINDRPSDVRQLAKWFRGKKVMINVLQYNPTSNSRIKAPQKREIVAFKHQLEQAGLEVTMRVSHGREINAACGQLANTYNKFKKK"}, "dna_sequence": {"accession": "CP160824.1", "fmin": "58137", "fmax": "59121", "strand": "-", "sequence": "ATGAAACGTTTACCTAAATATACGCCTGCGGAAGTACGGAATGATCCATACGGATTTACTTACAAAGAAATGTCGGAAGTTATTGGCGAGAATGAAGCAAAAGCCTTATATGAAGAATTATATAAGCAATTACCACGCAAAAAAAATCTATCAATGTTGGTAAAAAATATTTGCAAAAGCAGTGATACTGAAAAGTATGTTTACGAACTGAAAGACAACAAATACATTGAAACGGTTTTTATCAAGCGGCGAGATGGTGGAACTGTTTGCGTGAGCACACAAGTCGGTTGTCCTGTTGGTTGTATTTTTTGTGAGTCCGGGCGAAATGGCTTTGTTCGTAATCTAACATCGTCAGAAATCGTACAACAGATTATATTGTTGCGTCGAAAAGTAAACCGTATCGTTTTTATGGGTATGGGAGAGCCTTTATTCAATTATGACAACTTGATAAAAGCAATCCATATTCTCCGAGATAGATATGGGCTCAACTTTCCAACCGACGGCATTACCATATCAACAGTTGGTCCGGTCGATCAATTAAAAAAATTGCGCGAGGAACATCTTAAAATTCAGTTGACAATATCTTTACACGCAGCAACACAATCTGCAAGAAATCGTATTATTCCTCACATGCGCATATATGCTATTGAAGATGTTGTTAAGCAAGCCTTATCCTATTCTGAAAGGCATAATCGCAAAATTGTCTTTGCGTATTTGCTTTTACCGGGTATAAATGACCGGCCCTCAGATGTAAGACAACTTGCAAAATGGTTTCGGGGCAAAAAAGTTATGATTAACGTGTTACAATACAACCCAACAAGCAATTCAAGAATTAAAGCACCACAGAAACGGGAAATAGTTGCATTCAAACATCAATTAGAGCAAGCAGGACTTGAAGTTACTATGAGAGTTTCTCATGGCAGAGAGATTAACGCGGCTTGTGGACAGTTAGCTAACACATATAATAAATTCAAAAAAAAATGA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "36807", "NCBI_taxonomy_name": "Clostridioides difficile", "NCBI_taxonomy_id": "1496"}}}}, "ARO_accession": "3009654", "ARO_id": "48525", "ARO_name": "MrmA", "CARD_short_name": "MrmA", "ARO_description": "MrmA is a RlmN-like 23S rRNA adenine(2503)-methyltransferase identified from Clostridioides difficile and associated with increased resistance to erythromycin.", "ARO_category": {"36341": {"category_aro_accession": "3000202", "category_aro_cvterm_id": "36341", "category_aro_name": "Cfr-like 23S rRNA methyltransferase", "category_aro_description": "Cfr genes produce enzymes which catalyze the methylation of the 23S rRNA subunit at position 8 of adenine-2503. Methylation of 23S rRNA at this site confers resistance to some classes of antibiotics, including streptogramins, chloramphenicols, florfenicols, linezolids and clindamycin.", "category_aro_class_name": "AMR Gene Family"}, "35919": {"category_aro_accession": "0000000", "category_aro_cvterm_id": "35919", "category_aro_name": "macrolide antibiotic", "category_aro_description": "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.", "category_aro_class_name": "Drug Class"}, "35936": {"category_aro_accession": "0000017", "category_aro_cvterm_id": "35936", "category_aro_name": "lincosamide antibiotic", "category_aro_description": "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.", "category_aro_class_name": "Drug Class"}, "35945": {"category_aro_accession": "0000026", "category_aro_cvterm_id": "35945", "category_aro_name": "streptogramin antibiotic", "category_aro_description": "Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.", "category_aro_class_name": "Drug Class"}, "36218": {"category_aro_accession": "3000079", "category_aro_cvterm_id": "36218", "category_aro_name": "oxazolidinone antibiotic", "category_aro_description": "Oxazolidinones are a class of synthetic antibiotics discovered the the 1980's.  They inhibit protein synthesis by binding to domain V of the 23S rRNA of the 50S subunit of bacterial ribosomes.  Linezolid is the only member of this class currently in clinical use.", "category_aro_class_name": "Drug Class"}, "36526": {"category_aro_accession": "3000387", "category_aro_cvterm_id": "36526", "category_aro_name": "phenicol antibiotic", "category_aro_description": "Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.", "category_aro_class_name": "Drug Class"}, "35997": {"category_aro_accession": "0001001", "category_aro_cvterm_id": "35997", "category_aro_name": "antibiotic target alteration", "category_aro_description": "Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "8530": {"model_id": "8530", "model_name": "Mycobacterium tuberculosis fbiA with mutation conferring resistance to delamanid", "model_type": "protein variant model", "model_type_id": "40293", "model_description": "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.", "model_param": {"40494": {"param_type": "frameshift mutation", "param_description": "A frameshift is a sequence change between the translation initiation (start) and termination (stop) codon where, compared to a reference sequence, translation shifts to another reading frame as caused by nucleotide insertions and deletions. In ARO, these are annotated at the protein level with the first changed most N-terminal wildtype amino acid position. Format is given as [wildtype AA][position]fs, e.g. S531fs where S531 is a frameshifted coordinate beginning with codon 531. Termination may also be denoted as: Ter[position]fs.", "param_type_id": "40494", "param_value": {"18764": "V329fs"}}, "snp": {"WHO-R": {"18764": "D95Y"}}, "blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "600"}}, "model_sequences": {"sequence": {"11382": {"protein_sequence": {"accession": "NP_217778.1", "sequence": "MKVTVLAGGVGGARFLLGVQQLLGLGQFAANSAHSDADHQLSAVVNVGDDAWIHGLRVCPDLDTCMYTLGGGVDPQRGWGQRDETWHAMQELVRYGVQPDWFELGDRDLATHLVRTQMLQAGYPLSQITEALCDRWQPGARLLPATDDRCETHVVITDPVDESRKAIHFQEWWVRYRAQVPTHSFAFVGAEKSSAATEAIAALADADIIMLAPSNPVVSIGAILAVPGIRAALREATAPIVGYSPIIGEKPLRGMADTCLSVIGVDSTAAAVGRHYGARCATGILDCWLVHDGDHAEIDGVTVRSVPLLMTDPNATAEMVRAGCDLAGVVA"}, "dna_sequence": {"accession": "NC_000962.3", "fmin": "3640542", "fmax": "3641538", "strand": "+", "sequence": "GTGAAGGTCACCGTTCTGGCCGGTGGAGTCGGCGGCGCCCGCTTCCTGCTCGGGGTCCAGCAGCTGCTCGGCCTGGGCCAGTTTGCTGCCAATTCTGCCCACTCGGACGCCGACCACCAACTGAGCGCTGTCGTCAACGTCGGCGACGACGCCTGGATCCACGGGCTGCGTGTCTGCCCGGATCTGGACACCTGCATGTATACCCTGGGCGGCGGGGTGGACCCCCAGCGCGGCTGGGGCCAGCGTGACGAAACTTGGCACGCCATGCAGGAACTGGTGCGCTATGGCGTGCAGCCCGACTGGTTCGAGCTCGGGGACCGCGATCTGGCCACCCATCTGGTGCGCACCCAGATGCTGCAGGCCGGCTACCCCCTGTCACAGATCACCGAGGCCCTATGCGATCGCTGGCAACCGGGCGCCCGCTTGCTGCCTGCCACCGACGACCGTTGCGAAACCCATGTAGTGATCACCGACCCGGTCGACGAAAGCCGCAAGGCGATCCATTTTCAGGAGTGGTGGGTGCGCTACCGTGCCCAGGTGCCGACGCACAGCTTTGCTTTTGTCGGCGCTGAAAAGTCCAGCGCTGCAACCGAAGCGATCGCCGCCCTGGCCGACGCCGACATCATCATGCTGGCGCCGTCTAATCCGGTGGTCAGCATCGGCGCCATCCTGGCCGTCCCCGGGATTCGCGCGGCGTTGCGGGAAGCAACCGCACCGATCGTCGGCTACTCGCCGATCATCGGCGAAAAGCCGTTGCGCGGCATGGCCGATACGTGCCTTTCGGTTATCGGGGTGGATTCCACCGCGGCCGCTGTGGGCCGGCACTACGGCGCGCGGTGCGCCACCGGGATACTGGACTGCTGGCTGGTGCACGACGGCGACCACGCTGAGATTGACGGGGTGACGGTGCGGTCGGTGCCGCTGCTGATGACCGACCCGAACGCGACGGCTGAGATGGTTCGCGCCGGGTGCGACCTTGCGGGAGTGGTAGCTTGA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "39507", "NCBI_taxonomy_name": "Mycobacterium tuberculosis H37Rv", "NCBI_taxonomy_id": "83332"}}}}, "ARO_accession": "3009339", "ARO_id": "48197", "ARO_name": "Mycobacterium tuberculosis fbiA with mutation conferring resistance to delamanid", "CARD_short_name": "Mtub_fbiA_DLM", "ARO_description": "fbiA is an enzyme in the Coenzyme F420 biosynthesis pathway of Mycobacterium tuberculosis. Mutations in fbiA are associated with increased resistance to the antibiotic delamanid.", "ARO_category": {"48196": {"category_aro_accession": "3009338", "category_aro_cvterm_id": "48196", "category_aro_name": "antibiotic resistant F420 biosynthesis protein", "category_aro_description": "Antibiotic resistant variants of proteins associated with Coenzyme F420 biosynthesis.", "category_aro_class_name": "AMR Gene Family"}, "41239": {"category_aro_accession": "3004115", "category_aro_cvterm_id": "41239", "category_aro_name": "nitroimidazole antibiotic", "category_aro_description": "Nitroimidazoles are a group of drugs that have both antiprotozoal and antibacterial activity, classified with respect to the location of the nitro functional group.", "category_aro_class_name": "Drug Class"}, "35997": {"category_aro_accession": "0001001", "category_aro_cvterm_id": "35997", "category_aro_name": "antibiotic target alteration", "category_aro_description": "Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "8531": {"model_id": "8531", "model_name": "Mycobacterium tuberculosis fbiB with mutation conferring resistance to delamanid", "model_type": "protein variant model", "model_type_id": "40293", "model_description": "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.", "model_param": {"40494": {"param_type": "frameshift mutation", "param_description": "A frameshift is a sequence change between the translation initiation (start) and termination (stop) codon where, compared to a reference sequence, translation shifts to another reading frame as caused by nucleotide insertions and deletions. In ARO, these are annotated at the protein level with the first changed most N-terminal wildtype amino acid position. Format is given as [wildtype AA][position]fs, e.g. S531fs where S531 is a frameshifted coordinate beginning with codon 531. Termination may also be denoted as: Ter[position]fs.", "param_type_id": "40494", "param_value": {"18765": "V17fs"}}, "snp": {"WHO-R": {"18765": "D95Y"}}, "blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "800"}}, "model_sequences": {"sequence": {"11381": {"protein_sequence": {"accession": "NP_217779.1", "sequence": "MTGPEHGSASTIEILPVIGLPEFRPGDDLSAAVAAAAPWLRDGDVVVVTSKVVSKCEGRLVPAPEDPEQRDRLRRKLIEDEAVRVLARKDRTLITENRLGLVQAAAGVDGSNVGRSELALLPVDPDASAATLRAGLRERLGVTVAVVITDTMGRAWRNGQTDAAVGAAGLAVLRNYAGVRDPYGNELVVTEVAVADEIAAAADLVKGKLTATPVAVVRGFGVSDDGSTARQLLRPGANDLFWLGTAEALELGRQQAQLLRRSVRRFSTDPVPGDLVEAAVAEALTAPAPHHTRPTRFVWLQTPAIRARLLDRMKDKWRSDLTSDGLPADAIERRVARGQILYDAPEVVIPMLVPDGAHSYPDAARTDAEHTMFTVAVGAAVQALLVALAVRGLGSCWIGSTIFAADLVRDELDLPVDWEPLGAIAIGYADEPSGLRDPVPAADLLILK"}, "dna_sequence": {"accession": "NC_000962.3", "fmin": "3641534", "fmax": "3642881", "strand": "+", "sequence": "TTGACCGGCCCCGAACATGGCTCCGCCTCGACCATCGAGATCCTGCCCGTCATCGGGCTGCCCGAATTCCGTCCCGGCGACGATCTGAGCGCCGCCGTCGCCGCGGCGGCACCGTGGCTACGCGACGGTGACGTCGTGGTGGTTACCAGCAAGGTGGTGTCCAAATGCGAGGGCCGGCTGGTTCCGGCTCCCGAAGACCCCGAGCAAAGAGACCGATTGCGCCGCAAGCTGATCGAGGATGAGGCAGTGCGCGTGTTGGCGCGCAAGGACCGCACGTTGATCACCGAGAATCGACTCGGGCTGGTTCAGGCGGCCGCCGGCGTGGACGGATCCAACGTCGGCCGGTCCGAGTTAGCGCTGCTGCCGGTCGATCCTGACGCCAGTGCCGCAACCTTGCGCGCCGGGCTGCGCGAGCGGCTCGGCGTCACCGTCGCCGTGGTCATCACCGACACCATGGGACGCGCCTGGCGCAACGGCCAGACCGATGCCGCAGTCGGCGCTGCCGGTCTGGCGGTGCTGCGCAACTATGCCGGTGTCCGCGACCCATACGGCAATGAGTTGGTGGTCACCGAGGTCGCAGTCGCCGACGAGATCGCCGCGGCCGCCGACTTGGTCAAAGGCAAACTGACCGCGACGCCGGTGGCGGTGGTGCGTGGGTTCGGCGTGTCCGACGACGGCTCGACAGCCCGGCAACTGCTGCGGCCGGGCGCCAACGACCTGTTCTGGCTCGGGACCGCCGAAGCGCTCGAGCTGGGTCGCCAGCAAGCCCAACTGTTGCGCAGGTCCGTTCGCCGGTTTAGCACCGATCCGGTGCCGGGCGACCTCGTCGAGGCTGCGGTCGCCGAGGCCCTCACCGCGCCAGCCCCACATCACACCCGGCCGACCCGATTCGTGTGGCTGCAGACACCGGCCATCCGCGCGCGGCTGCTAGATCGGATGAAAGACAAGTGGCGGTCTGATCTCACCAGTGACGGCTTGCCCGCCGACGCGATAGAACGCCGGGTGGCACGCGGCCAGATCCTCTATGACGCACCCGAAGTCGTCATACCGATGCTGGTGCCCGACGGAGCACACAGCTACCCCGATGCCGCCCGCACCGACGCCGAGCACACCATGTTCACGGTCGCCGTCGGAGCGGCCGTACAAGCCTTGCTGGTCGCGCTGGCCGTGCGCGGGCTGGGCAGTTGCTGGATCGGCTCGACGATCTTTGCCGCTGACCTGGTCCGCGACGAGCTGGACCTGCCAGTCGACTGGGAGCCGTTGGGCGCCATCGCGATCGGATATGCCGACGAGCCGTCCGGGTTGCGCGACCCGGTGCCTGCCGCCGATTTGCTGATCCTGAAGTGA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "39507", "NCBI_taxonomy_name": "Mycobacterium tuberculosis H37Rv", "NCBI_taxonomy_id": "83332"}}}}, "ARO_accession": "3009340", "ARO_id": "48198", "ARO_name": "Mycobacterium tuberculosis fbiB with mutation conferring resistance to delamanid", "CARD_short_name": "Mtub_fbiB_DLM", "ARO_description": "fbiB is an enzyme in the Coenzyme F420 biosynthesis pathway of Mycobacterium tuberculosis. Mutations in fbiB are associated with increased resistance to the antibiotic delamanid.", "ARO_category": {"48196": {"category_aro_accession": "3009338", "category_aro_cvterm_id": "48196", "category_aro_name": "antibiotic resistant F420 biosynthesis protein", "category_aro_description": "Antibiotic resistant variants of proteins associated with Coenzyme F420 biosynthesis.", "category_aro_class_name": "AMR Gene Family"}, "41239": {"category_aro_accession": "3004115", "category_aro_cvterm_id": "41239", "category_aro_name": "nitroimidazole antibiotic", "category_aro_description": "Nitroimidazoles are a group of drugs that have both antiprotozoal and antibacterial activity, classified with respect to the location of the nitro functional group.", "category_aro_class_name": "Drug Class"}, "35997": {"category_aro_accession": "0001001", "category_aro_cvterm_id": "35997", "category_aro_name": "antibiotic target alteration", "category_aro_description": "Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "8532": {"model_id": "8532", "model_name": "Mycobacterium tuberculosis fbiC with mutation conferring resistance to delamanid", "model_type": "protein variant model", "model_type_id": "40293", "model_description": "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.", "model_param": {"40494": {"param_type": "frameshift mutation", "param_description": "A frameshift is a sequence change between the translation initiation (start) and termination (stop) codon where, compared to a reference sequence, translation shifts to another reading frame as caused by nucleotide insertions and deletions. In ARO, these are annotated at the protein level with the first changed most N-terminal wildtype amino acid position. Format is given as [wildtype AA][position]fs, e.g. S531fs where S531 is a frameshifted coordinate beginning with codon 531. Termination may also be denoted as: Ter[position]fs.", "param_type_id": "40494", "param_value": {"18772": "S443fs", "18767": "A487fs", "18768": "A639fs", "18771": "P362fs", "18769": "A855fs", "18770": "A856fs"}}, "snp": {"WHO-R": {"18772": "D95Y", "18767": "D95Y", "18768": "D95Y", "18771": "D95Y", "18769": "D95Y", "18770": "D95Y"}}, "blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "1650"}}, "model_sequences": {"sequence": {"11380": {"protein_sequence": {"accession": "NP_215689.1", "sequence": "MPQPVGRKSTALPSPVVPPQANASALRRVLRRARDGVTLNVDEAAIAMTARGDELADLCASAARVRDAGLVSAGRHGPSGRLAISYSRKVFIPVTRLCRDNCHYCTFVTVPGKLRAQGSSTYMEPDEILDVARRGAEFGCKEALFTLGDRPEARWRQAREWLGERGYDSTLSYVRAMAIRVLEQTGLLPHLNPGVMSWSEMSRLKPVAPSMGMMLETTSRRLFETKGLAHYGSPDKDPAVRLRVLTDAGRLSIPFTTGLLVGIGETLSERADTLHAIRKSHKEFGHIQEVIVQNFRAKEHTAMAAFPDAGIEDYLATVAVARLVLGPGMRIQAPPNLVSGDECRALVGAGVDDWGGVSPLTPDHVNPERPWPALDELAAVTAEAGYDMVQRLTAQPKYVQAGAAWIDPRVRGHVVALADPATGLARDVNPVGMPWQEPDDVASWGRVDLGAAIDTQGRNTAVRSDLASAFGDWESIREQVHELAVRAPERIDTDVLAALRSAERAPAGCTDGEYLALATADGPALEAVAALADSLRRDVVGDEVTFVVNRNINFTNICYTGCRFCAFAQRKGDADAYSLSVGEVADRAWEAHVAGATEVCMQGGIDPELPVTGYADLVRAVKARVPSMHVHAFSPMEIANGVTKSGLSIREWLIGLREAGLDTIPGTAAEILDDEVRWVLTKGKLPTSLWIEIVTTAHEVGLRSSSTMMYGHVDSPRHWVAHLNVLRDIQDRTGGFTEFVPLPFVHQNSPLYLAGAARPGPSHRDNRAVHALARIMLHGRISHIQTSWVKLGVRRTQVMLEGGANDLGGTLMEETISRMAGSEHGSAKTVAELVAIAEGIGRPARQRTTTYALLAA"}, "dna_sequence": {"accession": "NC_000962.3", "fmin": "1302930", "fmax": "1305501", "strand": "+", "sequence": "GTGCCGCAGCCTGTAGGTCGGAAGTCCACCGCTCTGCCGAGTCCCGTTGTACCGCCCCAGGCAAATGCCTCAGCGTTGCGGCGGGTACTGCGACGGGCCCGAGATGGTGTCACGCTGAACGTGGATGAGGCGGCCATAGCGATGACCGCACGCGGTGACGAGCTGGCCGACCTGTGCGCGAGCGCCGCGCGGGTGCGCGATGCGGGTCTCGTGTCGGCCGGCCGGCACGGGCCCAGCGGCAGGTTGGCGATCAGCTATTCGCGCAAGGTGTTTATCCCGGTCACCCGGTTATGCCGGGACAATTGCCACTATTGCACGTTCGTCACCGTGCCGGGCAAGCTACGCGCCCAAGGTTCCAGCACGTATATGGAACCCGACGAGATCCTCGACGTTGCCCGCCGAGGTGCCGAATTCGGTTGCAAGGAAGCGCTATTCACTCTCGGTGACCGTCCGGAGGCGCGTTGGCGCCAGGCACGCGAATGGCTCGGCGAACGGGGCTATGACTCCACGTTGTCCTACGTGCGCGCGATGGCAATCCGTGTGCTGGAGCAAACCGGGCTGTTGCCGCACCTGAACCCGGGTGTGATGAGCTGGTCGGAGATGTCGCGGCTCAAACCGGTGGCGCCGTCGATGGGCATGATGCTGGAGACGACCTCGCGACGGCTGTTCGAAACCAAGGGGCTCGCCCACTACGGCAGCCCTGACAAAGACCCGGCGGTGCGGCTGCGTGTCCTGACCGACGCCGGCCGGTTGTCCATTCCGTTTACCACCGGTCTGTTGGTCGGCATCGGCGAGACGCTATCCGAGCGCGCCGATACGTTACATGCGATTCGCAAGTCGCACAAGGAGTTCGGGCATATCCAAGAAGTGATCGTGCAGAACTTCCGCGCCAAGGAACACACCGCGATGGCCGCCTTCCCCGATGCCGGAATCGAGGATTACCTGGCGACGGTTGCGGTGGCGCGGCTGGTGCTGGGCCCGGGCATGCGCATCCAGGCGCCGCCGAACCTGGTGTCTGGCGACGAATGCCGGGCGCTGGTTGGCGCCGGGGTCGACGACTGGGGCGGTGTCTCACCGTTGACGCCCGACCATGTCAACCCCGAACGGCCCTGGCCCGCTTTGGACGAGCTGGCGGCGGTCACCGCCGAAGCCGGCTACGACATGGTGCAGCGGCTGACCGCGCAACCCAAATACGTACAGGCGGGCGCGGCGTGGATCGACCCGCGGGTGCGGGGACATGTGGTGGCGCTGGCGGATCCGGCGACCGGCCTGGCCCGCGACGTCAACCCGGTGGGCATGCCGTGGCAGGAGCCCGACGACGTGGCGTCCTGGGGCCGGGTCGATCTGGGCGCAGCGATCGACACTCAGGGCCGCAATACCGCAGTGCGCAGCGACCTGGCCAGCGCCTTCGGTGACTGGGAATCGATCCGCGAGCAGGTGCACGAGCTGGCGGTCCGCGCTCCGGAACGCATTGACACCGATGTGCTTGCCGCCCTGCGATCGGCGGAGCGTGCGCCCGCCGGCTGCACCGACGGCGAGTATCTGGCGCTTGCCACCGCCGACGGTCCTGCGCTGGAAGCCGTTGCCGCACTGGCTGATTCGTTGCGCCGCGATGTCGTCGGCGACGAGGTGACCTTTGTGGTCAACCGTAACATCAACTTCACCAACATCTGCTACACCGGTTGCCGGTTCTGCGCGTTCGCCCAGCGAAAGGGTGACGCCGACGCCTACTCGCTGTCGGTCGGAGAGGTCGCCGACCGGGCATGGGAGGCCCACGTCGCCGGGGCCACCGAAGTATGCATGCAGGGCGGTATCGATCCCGAGCTACCGGTCACCGGCTACGCCGATCTGGTTCGTGCCGTCAAGGCGCGGGTGCCCTCCATGCATGTGCACGCGTTTTCCCCGATGGAGATCGCCAACGGCGTCACCAAGAGCGGGCTGAGCATTCGCGAGTGGCTGATCGGCCTGCGCGAGGCCGGGCTGGATACCATCCCGGGTACCGCCGCGGAAATCCTGGACGACGAGGTTCGCTGGGTGCTGACCAAGGGCAAGCTGCCGACGTCATTGTGGATCGAAATCGTGACGACCGCCCACGAGGTGGGTCTGCGGTCATCATCGACGATGATGTACGGGCATGTGGACAGTCCACGGCACTGGGTCGCCCATCTTAACGTGCTGCGCGATATTCAGGACCGTACCGGCGGCTTCACCGAGTTCGTCCCGTTGCCGTTCGTGCACCAGAATTCACCGTTGTACCTGGCCGGTGCGGCGCGCCCCGGGCCCAGCCATCGCGACAACCGCGCGGTACATGCTTTGGCGCGGATCATGTTGCACGGCCGCATCTCGCACATTCAGACCAGCTGGGTGAAACTTGGAGTGCGGCGCACCCAGGTGATGCTCGAAGGTGGCGCCAACGACCTGGGCGGCACGCTGATGGAGGAGACCATCTCGCGGATGGCCGGTTCCGAACACGGATCGGCCAAGACCGTCGCTGAGCTGGTCGCGATCGCCGAAGGCATCGGCCGCCCGGCGCGCCAGCGCACTACCACATACGCCCTGCTTGCGGCCTAG", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "39507", "NCBI_taxonomy_name": "Mycobacterium tuberculosis H37Rv", "NCBI_taxonomy_id": "83332"}}}}, "ARO_accession": "3009341", "ARO_id": "48199", "ARO_name": "Mycobacterium tuberculosis fbiC with mutation conferring resistance to delamanid", "CARD_short_name": "Mtub_fbiC_DLM", "ARO_description": "fbiC is an enzyme in the Coenzyme F420 biosynthesis pathway of Mycobacterium tuberculosis. Mutations in fbiC are associated with increased resistance to the antibiotic delamanid.", "ARO_category": {"48196": {"category_aro_accession": "3009338", "category_aro_cvterm_id": "48196", "category_aro_name": "antibiotic resistant F420 biosynthesis protein", "category_aro_description": "Antibiotic resistant variants of proteins associated with Coenzyme F420 biosynthesis.", "category_aro_class_name": "AMR Gene Family"}, "41239": {"category_aro_accession": "3004115", "category_aro_cvterm_id": "41239", "category_aro_name": "nitroimidazole antibiotic", "category_aro_description": "Nitroimidazoles are a group of drugs that have both antiprotozoal and antibacterial activity, classified with respect to the location of the nitro functional group.", "category_aro_class_name": "Drug Class"}, "35997": {"category_aro_accession": "0001001", "category_aro_cvterm_id": "35997", "category_aro_name": "antibiotic target alteration", "category_aro_description": "Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "8533": {"model_id": "8533", "model_name": "Mycobacterium tuberculosis eis with mutation conferring resistance to amikacin", "model_type": "protein variant model", "model_type_id": "40293", "model_description": "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.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "725"}, "41339": {"param_type": "nucleotide substitution in promoter region", "param_description": "A nucleotide sequence change where, compared to a reference sequence, one nucleotide is replaced by one other nucleotide in the promoter region of a gene. These substitutions are indicated as upstream of the reference sequence transcription initiation site. Format is given by [-][position][wildtype][>][mutation], e.g. -11t>c or -15g>Var where Var represents any possible substitution.", "param_type_id": "41339", "param_value": {"19441": "-14c>t"}}, "snp": {"WHO-R": {"19441": "D95Y"}}}, "model_sequences": {"sequence": {"11378": {"protein_sequence": {"accession": "NP_216932.2", "sequence": "MTVTLCSPTEDDWPGMFLLAAASFTDFIGPESATAWRTLVPTDGAVVVRDGAGPGSEVVGMALYMDLRLTVPGEVVLPTAGLSFVAVAPTHRRRGLLRAMCAELHRRIADSGYPVAALHASEGGIYGRFGYGPATTLHELTVDRRFARFHADAPGGGLGGSSVRLVRPTEHRGEFEAIYERWRQQVPGGLLRPQVLWDELLAECKAAPGGDRESFALLHPDGYALYRVDRTDLKLARVSELRAVTADAHCALWRALIGLDSMERISIITHPQDPLPHLLTDTRLARTTWRQDGLWLRIMNVPAALEARGYAHEVGEFSTVLEVSDGGRFALKIGDGRARCTPTDAAAEIEMDRDVLGSLYLGAHRASTLAAANRLRTKDSQLLRRLDAAFASDVPVQTAFEF"}, "dna_sequence": {"accession": "NC_000962.3", "fmin": "2714123", "fmax": "2715332", "strand": "-", "sequence": "GTGACTGTGACCCTGTGTAGCCCGACCGAGGACGACTGGCCGGGGATGTTCCTACTGGCCGCGGCCAGTTTCACCGATTTCATCGGCCCTGAATCAGCGACCGCCTGGCGGACCCTGGTGCCCACCGACGGAGCGGTGGTGGTCCGCGATGGTGCCGGCCCGGGTTCTGAGGTGGTCGGGATGGCGCTGTACATGGATCTGCGGTTGACGGTGCCTGGTGAAGTGGTGCTCCCGACCGCCGGTCTCAGTTTCGTCGCGGTGGCGCCGACGCATCGCCGGCGCGGCTTGCTGCGCGCGATGTGCGCCGAACTGCACCGCCGCATAGCCGATTCCGGCTATCCGGTCGCGGCACTGCATGCTAGCGAGGGCGGCATCTACGGCCGGTTCGGCTACGGGCCCGCTACCACCTTGCATGAGCTGACGGTCGACCGACGCTTCGCGCGCTTTCACGCCGACGCACCGGGCGGCGGCCTAGGTGGCAGCAGCGTCCGGTTGGTCAGACCCACCGAGCATCGCGGCGAGTTTGAGGCGATCTACGAGCGATGGCGCCAGCAGGTGCCGGGCGGGCTGCTACGCCCGCAGGTGCTCTGGGACGAGCTGCTGGCAGAATGCAAAGCCGCGCCCGGTGGAGACCGTGAATCGTTCGCGTTACTGCATCCCGACGGGTACGCGCTGTACCGGGTGGATCGCACCGATCTCAAGCTAGCGCGCGTCAGCGAACTCAGGGCGGTAACCGCAGATGCGCATTGTGCGTTGTGGCGGGCCCTGATTGGCCTCGACTCCATGGAGCGAATCAGCATCATCACCCATCCACAGGACCCGTTACCCCACCTGCTCACCGATACCCGACTGGCCCGCACTACCTGGCGCCAGGACGGCCTGTGGTTGCGCATCATGAACGTACCGGCCGCACTCGAGGCGCGTGGTTACGCTCACGAAGTTGGCGAGTTTTCCACGGTCCTCGAGGTATCCGATGGCGGCCGGTTCGCGCTCAAGATCGGTGACGGCCGTGCGCGGTGTACCCCGACCGATGCGGCAGCCGAGATCGAAATGGATCGGGACGTACTGGGCAGCCTTTACCTTGGAGCGCACCGCGCTTCGACGTTAGCCGCCGCTAACCGGTTGCGCACCAAAGATTCCCAGCTGCTTCGTCGACTCGACGCGGCGTTTGCCAGTGATGTTCCCGTCCAGACCGCGTTCGAGTTCTGA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "39507", "NCBI_taxonomy_name": "Mycobacterium tuberculosis H37Rv", "NCBI_taxonomy_id": "83332"}}}}, "ARO_accession": "3009333", "ARO_id": "48190", "ARO_name": "Mycobacterium tuberculosis eis with mutation conferring resistance to amikacin", "CARD_short_name": "Mtub_eis_AMK", "ARO_description": "Mutations in Mycobacterium tuberculosis eis that contribute to or confer resistance to amikacin.", "ARO_category": {"48189": {"category_aro_accession": "3009332", "category_aro_cvterm_id": "48189", "category_aro_name": "amikacin-resistant eis", "category_aro_description": "Variants of the enhanced intracellular survival protein eis which are associated with increased resistance to amikacin.", "category_aro_class_name": "AMR Gene Family"}, "35935": {"category_aro_accession": "0000016", "category_aro_cvterm_id": "35935", "category_aro_name": "aminoglycoside antibiotic", "category_aro_description": "Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.", "category_aro_class_name": "Drug Class"}, "35997": {"category_aro_accession": "0001001", "category_aro_cvterm_id": "35997", "category_aro_name": "antibiotic target alteration", "category_aro_description": "Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "8527": {"model_id": "8527", "model_name": "Mycobacterium tuberculosis Rv2535c with mutation conferring resistance to clofazimine", "model_type": "protein variant model", "model_type_id": "40293", "model_description": "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.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "700"}, "40494": {"param_type": "frameshift mutation", "param_description": "A frameshift is a sequence change between the translation initiation (start) and termination (stop) codon where, compared to a reference sequence, translation shifts to another reading frame as caused by nucleotide insertions and deletions. In ARO, these are annotated at the protein level with the first changed most N-terminal wildtype amino acid position. Format is given as [wildtype AA][position]fs, e.g. S531fs where S531 is a frameshifted coordinate beginning with codon 531. Termination may also be denoted as: Ter[position]fs.", "param_type_id": "40494", "param_value": {"18709": "D232fs", "18711": "H100fs", "18712": "L317fs", "18713": "V273fs", "18710": "D51fs"}}, "snp": {"WHO-R": {"18709": "D95Y", "18711": "D95Y", "18712": "D95Y", "18713": "D95Y", "18710": "D95Y"}}}, "model_sequences": {"sequence": {"11371": {"protein_sequence": {"accession": "NP_217051.1", "sequence": "MTHSQRRDKLKAQIAASGLDAMLISDLINVRYLSGFSGSNGALLVFADERDAVLATDGRYRTQAASQAPDLEVAIERAVGRYLAGRAGEAGVGKLGFESHVVTVDGLDALAGALEGKNTELVRASGTVESLREVKDAGELALLRLACEAADAALTDLVARGGLRPGRTERQVSRELEALMLDHGADAVSFETIVAAGANSAIPHHRPTDAVLQVGDFVKIDFGALVAGYHSDMTRTFVLGKAADWQLEIYQLVAEAQQAGRQALLPGAELRGVDAAARQLIADAGYGEHFGHGLGHGVGLQIHEAPGIGVTSAGTLLAGSVVTVEPGVYLPGRGGVRIEDTLVVAGGTPKMPETAGQTPELLTRFPKELAIL"}, "dna_sequence": {"accession": "NC_000962.3", "fmin": "2859299", "fmax": "2860418", "strand": "-", "sequence": "GTGACACATTCCCAGCGTCGAGACAAGCTGAAAGCACAAATCGCTGCCTCCGGGTTGGATGCGATGCTGATCAGCGACCTGATAAACGTGCGATATCTATCAGGCTTCAGCGGGTCCAACGGCGCATTGCTGGTGTTCGCCGATGAGCGCGATGCCGTGTTGGCCACCGACGGCCGGTACCGCACTCAGGCCGCCTCGCAAGCGCCCGACCTCGAAGTGGCTATCGAGCGCGCGGTCGGGCGCTACCTGGCCGGCCGGGCCGGCGAGGCCGGCGTGGGAAAGCTGGGCTTCGAGAGCCACGTGGTCACGGTGGACGGCCTGGACGCCTTGGCGGGCGCGCTGGAGGGCAAGAACACCGAGTTGGTGCGGGCATCCGGAACTGTGGAGTCACTGCGCGAGGTTAAAGACGCCGGCGAGCTGGCGCTGCTGCGACTAGCCTGCGAAGCAGCCGATGCCGCGCTGACCGACTTGGTGGCCCGCGGCGGCCTGCGGCCGGGCCGAACCGAACGGCAGGTGAGCCGCGAGCTGGAGGCCCTGATGCTCGATCATGGCGCTGACGCGGTGTCATTCGAGACGATCGTGGCTGCCGGGGCCAATTCGGCGATCCCGCACCACCGGCCGACCGACGCGGTGCTGCAGGTCGGCGATTTCGTGAAGATCGACTTCGGCGCCCTGGTCGCCGGGTACCACTCCGATATGACCCGCACCTTCGTGTTGGGCAAGGCCGCCGACTGGCAGCTAGAGATCTATCAGCTGGTGGCCGAGGCGCAACAGGCCGGTCGGCAGGCGTTGCTGCCGGGTGCCGAGCTGCGGGGGGTGGACGCTGCAGCGCGCCAGCTGATCGCCGACGCCGGCTACGGCGAGCACTTCGGTCACGGACTGGGACACGGTGTTGGCCTGCAGATACATGAAGCGCCGGGCATCGGGGTCACATCCGCCGGTACACTACTGGCGGGCTCCGTGGTGACCGTGGAGCCCGGTGTCTATTTACCCGGCCGCGGCGGTGTCCGCATCGAGGACACATTGGTAGTGGCTGGCGGGACGCCGAAAATGCCTGAAACCGCCGGGCAGACCCCGGAATTGTTGACCCGGTTCCCCAAAGAACTGGCCATTCTGTAG", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "39507", "NCBI_taxonomy_name": "Mycobacterium tuberculosis H37Rv", "NCBI_taxonomy_id": "83332"}}}}, "ARO_accession": "3009335", "ARO_id": "48192", "ARO_name": "Mycobacterium tuberculosis Rv2535c with mutation conferring resistance to clofazimine", "CARD_short_name": "Mtub_pepQ_CFZ", "ARO_description": "These pepQ/Rv2535c mutations increase efflux through the mmpL5-mmpS5 (Rv0676c-Rv0677c) transporter, such as preventing degradation of MmpL5, which leads to reduced susceptibility to bedaquiline and clofazimine.", "ARO_category": {"48191": {"category_aro_accession": "3009334", "category_aro_cvterm_id": "48191", "category_aro_name": "clofazimine resistant Rv2535c", "category_aro_description": "Loss-of-function mutations in Rv2535c (pepQ) in Mycobacterium and Mycobacteroides which are associated with resistance to clofazimine.", "category_aro_class_name": "AMR Gene Family"}, "36012": {"category_aro_accession": "3000003", "category_aro_cvterm_id": "36012", "category_aro_name": "antibiotic without defined classification", "category_aro_description": "These compounds are antibiotics of unique structure or origin, without a defined classification.", "category_aro_class_name": "Drug Class"}, "35997": {"category_aro_accession": "0001001", "category_aro_cvterm_id": "35997", "category_aro_name": "antibiotic target alteration", "category_aro_description": "Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "8535": {"model_id": "8535", "model_name": "KPC-20", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "550"}}, "model_sequences": {"sequence": {"11383": {"protein_sequence": {"accession": "WP_436452774.1", "sequence": "MSLYRRLVLLSCLSWPLAGFSATALTNLIAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"}, "dna_sequence": {"accession": "NG_245797.1", "fmin": "100", "fmax": "982", "strand": "+", "sequence": "ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCATCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "41220", "NCBI_taxonomy_name": "Citrobacter youngae", "NCBI_taxonomy_id": "133448"}}}}, "ARO_accession": "3003144", "ARO_id": "39721", "ARO_name": "KPC-20", "CARD_short_name": "KPC-20", "ARO_description": "KPC-20 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.", "ARO_category": {"36198": {"category_aro_accession": "3000059", "category_aro_cvterm_id": "36198", "category_aro_name": "KPC beta-lactamase", "category_aro_description": "Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.", "category_aro_class_name": "AMR Gene Family"}, "35923": {"category_aro_accession": "0000004", "category_aro_cvterm_id": "35923", "category_aro_name": "monobactam", "category_aro_description": "Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam 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.", "category_aro_class_name": "Drug Class"}, "35939": {"category_aro_accession": "0000020", "category_aro_cvterm_id": "35939", "category_aro_name": "carbapenem", "category_aro_description": "Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem 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.", "category_aro_class_name": "Drug Class"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin 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.", "category_aro_class_name": "Drug Class"}, "36017": {"category_aro_accession": "3000008", "category_aro_cvterm_id": "36017", "category_aro_name": "penicillin beta-lactam", "category_aro_description": "Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like 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.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "8537": {"model_id": "8537", "model_name": "VIM-92", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"11386": {"protein_sequence": {"accession": "XKB79100.1", "sequence": "MFKLLSKLLVYLTASIMAIASPLAFSVDSSGEYPTVSEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEVEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSASVLYGGCAIYELSRTSAGNVADADLAEWPTSIERIQQHYPEAQFIIPGHGLPGGLDLLKHTTNVVKAHTNRSVVE"}, "dna_sequence": {"accession": "PQ563311.1", "fmin": "0", "fmax": "801", "strand": "+", "sequence": "ATGTTCAAACTTTTGAGTAAGTTATTGGTCTATTTGACCGCGTCTATCATGGCTATTGCGAGTCCGCTCGCTTTTTCCGTAGATTCTAGCGGTGAGTATCCGACAGTCAGCGAAATTCCGGTCGGGGAGGTCCGGCTTTACCAGATTGCCGATGGTGTTTGGTCGCATATCGCAACGCAGTCGTTTGATGGCGCAGTCTACCCGTCCAATGGTCTCATTGTCCGTGATGGTGATGAGTTGCTTTTGATTGATACAGCGTGGGGTGCGAAAAACACAGCGGCACTTCTCGCGGAGATTGAGAAGCAAATTGGACTTCCTGTAACGCGTGCAGTCTCCACGCACTTTCATGACGACCGCGTCGGCGGCGTTGATGTCCTTCGGGCGGCTGGGGTGGCAACGTACGCATCACCGTCGACACGCCGGCTAGCCGAGGTAGAGGGGAACGAGATTCCCACGCACTCTCTAGAAGGACTCTCATCGAGCGGGGACGCAGTGCGCTTCGGTCCAGTAGAACTCTTCTATCCTGGTGCTGCGCATTCGACCGACAACTTAGTTGTGTACGTCCCGTCTGCGAGTGTGCTCTATGGTGGTTGTGCGATTTATGAGTTGTCACGCACGTCTGCGGGGAACGTGGCCGATGCCGATCTGGCTGAATGGCCCACCTCCATTGAGCGGATTCAACAACACTACCCGGAAGCACAGTTCATCATTCCGGGGCACGGCCTGCCGGGCGGTCTAGACTTGCTCAAGCACACAACGAATGTTGTAAAAGCGCACACAAATCGCTCAGTCGTTGAGTAG", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "36752", "NCBI_taxonomy_name": "Pseudomonas aeruginosa", "NCBI_taxonomy_id": "287"}}}}, "ARO_accession": "3009643", "ARO_id": "48504", "ARO_name": "VIM-92", "CARD_short_name": "VIM-92", "ARO_description": "VIM-92 is a subclass B1 metallo-beta-lactamase identified from Pseudomonas aeruginosa and shown to confer resistance to carbapenem antibiotics.", "ARO_category": {"36030": {"category_aro_accession": "3000021", "category_aro_cvterm_id": "36030", "category_aro_name": "VIM beta-lactamase", "category_aro_description": "The Verone integron-encoded metallo-beta-lactamase (VIM) family was reported from Italy in 1999. There are, to date, 23 reported variants.  VIM enzymes mostly occur in P. aeruginosa, also P. putida and, very rarely, Enterobacteriaceae. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.  There is a strong incidence of these in East Asia.", "category_aro_class_name": "AMR Gene Family"}, "35939": {"category_aro_accession": "0000020", "category_aro_cvterm_id": "35939", "category_aro_name": "carbapenem", "category_aro_description": "Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem 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.", "category_aro_class_name": "Drug Class"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin 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.", "category_aro_class_name": "Drug Class"}, "36017": {"category_aro_accession": "3000008", "category_aro_cvterm_id": "36017", "category_aro_name": "penicillin beta-lactam", "category_aro_description": "Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like 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.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "8538": {"model_id": "8538", "model_name": "AMM-1", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"11388": {"protein_sequence": {"accession": "MFS1702987.1", "sequence": "MKALLTLVLTGLISLFPLLSYAENLTITAINDTVFLHQSSRQVEGYGAVTGNGLIVVNGAEAYLVDTPWDRDDIGVIQKWLEQRSLSLAGVIATHSHDDAGGNLDVFNQQHIPTWAHALTNEFLQEKGEQPATHMFTESDTVLTDTIEVFYPGPGHTLDNIVVWLPKQHVLFGGCFIRAMETNSMGYTAEGDVVQWGASAQRVLDRYRDIDTVVPGHGETGSVEMIRKTQRMAQQAAADILNQ"}, "dna_sequence": {"accession": "JBLBUE010000039.1", "fmin": "8598", "fmax": "9330", "strand": "-", "sequence": "ATGAAAGCATTGTTAACGTTGGTTCTGACAGGGCTGATTAGTCTGTTCCCATTGCTTAGTTATGCGGAAAATCTCACCATTACGGCCATTAATGACACCGTATTTTTACATCAGTCATCCCGTCAGGTTGAAGGTTATGGCGCCGTAACCGGCAATGGGTTAATTGTGGTAAACGGTGCGGAAGCTTATCTGGTAGACACGCCTTGGGATCGCGATGATATTGGCGTTATCCAGAAGTGGCTTGAGCAGCGCTCACTGAGCCTGGCAGGTGTTATTGCTACGCACTCTCACGACGACGCTGGCGGCAACCTGGATGTATTTAACCAACAACACATCCCCACCTGGGCACACGCACTTACCAATGAATTTTTGCAAGAAAAGGGTGAACAGCCTGCAACGCATATGTTTACCGAATCAGATACGGTTTTAACTGACACTATCGAAGTGTTTTATCCGGGGCCAGGACATACGCTGGACAATATCGTCGTGTGGCTGCCCAAACAGCATGTGTTGTTCGGCGGCTGCTTTATACGCGCAATGGAAACCAACTCCATGGGGTACACAGCTGAAGGCGATGTAGTCCAGTGGGGGGCGTCAGCTCAACGTGTATTGGACAGGTATCGCGATATTGATACCGTTGTGCCCGGGCACGGCGAGACAGGCTCGGTTGAAATGATCAGGAAAACACAGCGTATGGCGCAGCAAGCGGCTGCTGACATTCTTAACCAGTAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "48507", "NCBI_taxonomy_name": "Alteromonas sp. AMM-1", "NCBI_taxonomy_id": "3394233"}}}}, "ARO_accession": "3009645", "ARO_id": "48506", "ARO_name": "AMM-1", "CARD_short_name": "AMM-1", "ARO_description": "A subclass B1 metallo-beta-lactamase in the AMM family, identified from a metagenome-assembled genome of Alteromonas mangrovi.", "ARO_category": {"48505": {"category_aro_accession": "3009644", "category_aro_cvterm_id": "48505", "category_aro_name": "AMM beta-lactamase", "category_aro_description": "A subclass B1 metallo-beta-lactamase family originally identified from metagenomic assembly of Alteromonas mangrovi. These chromosomal resistance genes have been shown to confer resistance to carbapenem antibiotics.", "category_aro_class_name": "AMR Gene Family"}, "35939": {"category_aro_accession": "0000020", "category_aro_cvterm_id": "35939", "category_aro_name": "carbapenem", "category_aro_description": "Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem 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.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "8539": {"model_id": "8539", "model_name": "AMM-2", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"11389": {"protein_sequence": {"accession": "TPV56906.1", "sequence": "MKALLTLVLTGLISLFPLLSYAENLTIRAINDTVFLHQSSRQVEGYGAVTGNGLIVVTGAEAYLVDTPWDRDDIGVIQKWLEQRSLHLAGVIATHSHDDAGGNLDVFNQQHIPTWAHALTNEFLQEKGEQPATHMFTDSDTVLTDTIEVFYPGPGHTLDNIVVWLPKQHVLFGGCFIRAMETNSMGYTAEGDVVQWGASAQRVLDRYRDIDTVVPGHGETGSVEMIKKTQRMAKQAAAAILNQ"}, "dna_sequence": {"accession": "VHIP01000008.1", "fmin": "154577", "fmax": "155309", "strand": "-", "sequence": "ATGAAAGCGTTGTTAACGTTGGTTCTGACAGGGCTGATTAGTCTGTTCCCATTGCTGAGTTATGCGGAAAATCTCACCATTAGGGCCATTAATGACACCGTATTTTTACATCAGTCATCCCGTCAGGTTGAAGGTTATGGCGCCGTAACCGGCAACGGGTTAATTGTGGTAACCGGTGCGGAAGCTTATCTGGTAGACACGCCTTGGGATCGCGATGATATTGGCGTTATCCAGAAGTGGCTTGAGCAGCGCTCGCTGCACCTGGCAGGTGTTATTGCTACGCACTCTCACGACGACGCTGGCGGCAACCTGGATGTATTTAACCAACAACACATCCCCACCTGGGCTCATGCGCTTACCAATGAGTTTTTGCAAGAAAAAGGCGAACAGCCTGCAACGCATATGTTTACCGATTCAGATACGGTTCTAACTGACACTATTGAAGTGTTTTATCCGGGGCCAGGACATACGCTGGACAATATCGTCGTGTGGCTGCCCAAACAGCATGTGTTGTTCGGCGGCTGCTTTATACGCGCAATGGAAACCAACTCCATGGGGTACACAGCTGAAGGCGATGTAGTCCAGTGGGGGGCGTCAGCTCAACGTGTATTGGACAGGTATCGCGATATTGATACCGTTGTGCCCGGGCACGGCGAGACAGGCTCGGTTGAAATGATTAAGAAAACACAGCGCATGGCGAAGCAAGCGGCTGCTGCCATTCTTAACCAGTAA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "48509", "NCBI_taxonomy_name": "Aestuariibacter sp. GS-14", "NCBI_taxonomy_id": "2590670"}}}}, "ARO_accession": "3009646", "ARO_id": "48508", "ARO_name": "AMM-2", "CARD_short_name": "AMM-2", "ARO_description": "A subclass B1 metallo-beta-lactamase in the AMM family, identified from a metagenome-assembled genome of Alteromonas mangrovi.", "ARO_category": {"48505": {"category_aro_accession": "3009644", "category_aro_cvterm_id": "48505", "category_aro_name": "AMM beta-lactamase", "category_aro_description": "A subclass B1 metallo-beta-lactamase family originally identified from metagenomic assembly of Alteromonas mangrovi. These chromosomal resistance genes have been shown to confer resistance to carbapenem antibiotics.", "category_aro_class_name": "AMR Gene Family"}, "35939": {"category_aro_accession": "0000020", "category_aro_cvterm_id": "35939", "category_aro_name": "carbapenem", "category_aro_description": "Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem 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.", "category_aro_class_name": "Drug Class"}, "36000": {"category_aro_accession": "0001004", "category_aro_cvterm_id": "36000", "category_aro_name": "antibiotic inactivation", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance.", "category_aro_class_name": "Resistance Mechanism"}}}, "8540": {"model_id": "8540", "model_name": "erm(55)", "model_type": "protein homolog model", "model_type_id": "40292", "model_description": "Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.", "model_param": {"blastp_bit_score": {"param_type": "BLASTP bit-score", "param_description": "The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).", "param_type_id": "40725", "param_value": "500"}}, "model_sequences": {"sequence": {"11390": {"protein_sequence": {"accession": "WHP53453.1", "sequence": "MPTFRAGRHEFGQNFLTDQPTIDHIVKLVSQSNGPIIEIGSGAGALTLPMQTLLRPITAVEIDPRQVQALRRQVNSRTTVVHDDFLHFRLPRSPHTIVGNLPFHQTTAMLRRILHSDHWTTAVLLVQWEVARRRAAVGGATMMTAQSWPWYTFQLVGRIPAAAFTPRPGVDAGLMTITRRTVPLVNTAQRKQYSAFVHAVFTSKGSGLRQILPRVADASAKGGVMTWITQQRLSNSSLPRDLTPEQWAEIFAIATRHAAAATPKRSRNGR"}, "dna_sequence": {"accession": "OQ656455.1", "fmin": "319", "fmax": "1132", "strand": "+", "sequence": "ATGCCTACTTTCCGTGCTGGCCGCCACGAATTCGGCCAGAACTTCTTGACTGACCAACCGACGATCGACCACATTGTCAAACTCGTCTCGCAAAGCAACGGTCCGATCATCGAAATTGGTTCCGGCGCAGGGGCATTGACGCTTCCAATGCAAACCCTGCTACGGCCTATCACGGCCGTCGAGATAGACCCGCGACAGGTCCAAGCGCTCCGACGCCAGGTGAACTCGCGAACAACCGTTGTGCATGATGACTTCCTACACTTTCGACTACCGCGATCGCCGCACACCATCGTGGGAAACTTGCCATTCCACCAGACCACCGCGATGCTTCGGCGCATCCTGCACTCCGACCACTGGACGACCGCAGTCCTGCTCGTGCAGTGGGAGGTCGCGCGCCGCCGCGCAGCAGTGGGAGGCGCGACTATGATGACGGCGCAAAGCTGGCCGTGGTATACGTTCCAACTGGTTGGCCGCATTCCAGCAGCGGCATTCACACCCCGGCCGGGAGTCGATGCCGGCCTGATGACCATCACCCGGCGCACCGTCCCCCTCGTGAACACCGCCCAGCGCAAGCAATACAGCGCGTTCGTCCACGCCGTCTTCACAAGCAAAGGCAGCGGTCTGCGTCAGATTCTGCCGCGCGTCGCCGACGCCTCGGCGAAAGGTGGGGTCATGACATGGATTACACAGCAGCGACTCTCAAATTCATCTCTGCCTCGTGATCTCACGCCAGAGCAGTGGGCCGAGATCTTCGCCATCGCCACTCGACACGCTGCAGCAGCCACTCCCAAACGTTCGAGGAACGGGCGATGA", "partial": "0"}, "NCBI_taxonomy": {"NCBI_taxonomy_cvterm_id": "41314", "NCBI_taxonomy_name": "Mycobacteroides chelonae", "NCBI_taxonomy_id": "1774"}}}}, "ARO_accession": "3009647", "ARO_id": "48510", "ARO_name": "erm(55)", "CARD_short_name": "erm(55)", "ARO_description": "erm(55) is a plasmid-borne 23S rRNA methyltransferase identified from Mycobacterium chelonae.", "ARO_category": {"36699": {"category_aro_accession": "3000560", "category_aro_cvterm_id": "36699", "category_aro_name": "Erm-like 23S rRNA methyltransferase", "category_aro_description": "Erm proteins are part of the RNA methyltransferase family and methylate A2058 (E. coli numbering) of the 23S ribosomal RNA conferring degrees of resistance to Macrolides, Lincosamides and Streptogramin. This is called the MLS phenotype.", "category_aro_class_name": "AMR Gene Family"}, "35919": {"category_aro_accession": "0000000", "category_aro_cvterm_id": "35919", "category_aro_name": "macrolide antibiotic", "category_aro_description": "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.", "category_aro_class_name": "Drug Class"}, "35936": {"category_aro_accession": "0000017", "category_aro_cvterm_id": "35936", "category_aro_name": "lincosamide antibiotic", "category_aro_description": "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.", "category_aro_class_name": "Drug Class"}, "35945": {"category_aro_accession": "0000026", "category_aro_cvterm_id": "35945", "category_aro_name": "streptogramin antibiotic", "category_aro_description": "Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.", "category_aro_class_name": "Drug Class"}, "35997": {"category_aro_accession": "0001001", "category_aro_cvterm_id": "35997", "category_aro_name": "antibiotic target alteration", "category_aro_description": "Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.", "category_aro_class_name": "Resistance Mechanism"}}}}, "$update": {"2": {"$update": {"ARO_category": {"$delete": ["41256"]}}}, "5": {"$update": {"ARO_category": {"$delete": ["36327"]}}}, "7": {"$update": {"ARO_category": {"$insert": {"46264": {"category_aro_accession": "3007495", "category_aro_cvterm_id": "46264", "category_aro_name": "azole antibiotic", "category_aro_description": "Azoles are a group of antibiotics, particularly antifungals, that target the cytochrome P450 enzyme sterol 14alpha-demethylase, which converts lanosterol to ergosterol. 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Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam 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.", "category_aro_class_name": "Drug Class"}, "35939": {"category_aro_accession": "0000020", "category_aro_cvterm_id": "35939", "category_aro_name": "carbapenem", "category_aro_description": "Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. 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The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}, "36017": {"category_aro_accession": "3000008", "category_aro_cvterm_id": "36017", "category_aro_name": "penicillin beta-lactam", "category_aro_description": "Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like 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.", "category_aro_class_name": "Drug Class"}, "36189": {"category_aro_accession": "3000050", "category_aro_cvterm_id": "36189", "category_aro_name": "tetracycline antibiotic", "category_aro_description": "These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.", "category_aro_class_name": "Drug Class"}, "36192": {"category_aro_accession": "3000053", "category_aro_cvterm_id": "36192", "category_aro_name": "peptide antibiotic", "category_aro_description": "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.", "category_aro_class_name": "Drug Class"}, "36242": {"category_aro_accession": "3000103", "category_aro_cvterm_id": "36242", "category_aro_name": "aminocoumarin antibiotic", "category_aro_description": "Aminocoumarin antibiotics bind DNA gyrase subunit B to inhibit ATP-dependent DNA supercoiling.", "category_aro_class_name": "Drug Class"}, "36310": {"category_aro_accession": "3000171", "category_aro_cvterm_id": "36310", "category_aro_name": "diaminopyrimidine antibiotic", "category_aro_description": "Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.", "category_aro_class_name": "Drug Class"}, "36421": {"category_aro_accession": "3000282", "category_aro_cvterm_id": "36421", "category_aro_name": "sulfonamide antibiotic", "category_aro_description": "Sulfonamides are broad spectrum, synthetic antibiotics that contain the sulfonamide group. Sulfonamides inhibit dihydropteroate synthase, which catalyzes the conversion of p-aminobenzoic acid to dihydropteroic acid as part of the tetrahydrofolic acid biosynthetic pathway. Tetrahydrofolic acid is essential for folate synthesis, a precursor of many nucleotides and amino acids. Many sulfamides are taken with trimethoprim, an inhibitor of dihydrofolate reductase, also disturbing the trihydrofolic acid synthesis pathway.", "category_aro_class_name": "Drug Class"}, "36526": {"category_aro_accession": "3000387", "category_aro_cvterm_id": "36526", "category_aro_name": "phenicol antibiotic", "category_aro_description": "Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.", "category_aro_class_name": "Drug Class"}, "48528": {"category_aro_accession": "3009657", "category_aro_cvterm_id": "48528", "category_aro_name": "nonribosomal peptide antibiotics", "category_aro_description": "Nonribosomal peptide antibiotics are peptide natural products synthesized by nonribosomal peptide synthetases (NRPSs), rather than by the ribosome. They often contain non-proteinogenic amino acids and diverse chemical modifications that contribute to their structural and functional diversity.", "category_aro_class_name": "Drug Class"}}, "$delete": ["36298"]}}}, "458": {"$update": {"ARO_category": {"$delete": ["35968", "36298"]}}}, "402": {"$update": {"ARO_category": {"$delete": ["35968", "36298"]}}}, "336": {"$update": {"model_name": "tlrB", "ARO_name": "tlrB", "CARD_short_name": "tlrB", "ARO_category": {"$update": {"37697": {"$update": {"category_aro_name": "TlrA-like 23S rRNA methyltransferase", "category_aro_description": "23S ribosomal RNA methyltransferases modify guanosine 748 (E. coli numbering) to confer resistance to some macrolides and lincosamides."}}}, "$delete": ["36284"]}}}, "276": {"$update": {"ARO_category": {"$insert": {"48501": {"category_aro_accession": "3009640", "category_aro_cvterm_id": "48501", "category_aro_name": "antibiotic efflux regulatory protein", "category_aro_description": "Gene products that regulate efflux of antibiotics from cells.", "category_aro_class_name": "AMR Gene Family"}}, "$delete": ["35968", "36298", "36590"]}}}, "395": {"$update": {"ARO_category": {"$delete": ["35981"]}}}, "473": {"$update": {"ARO_category": {"$delete": ["35925", "35946", "35982", "36284", "36297"]}}}, "486": {"$update": {"ARO_category": {"$delete": ["36524", "36298"]}}}, "487": {"$update": {"ARO_category": {"$delete": ["35925", "36298"]}}}, "490": {"$update": {"ARO_category": {"$delete": ["35977", "36981"]}}}, "392": {"$update": {"ARO_category": {"$delete": ["35981", "35995", "40523"]}}}, "442": {"$update": {"ARO_category": {"$insert": {"36189": {"category_aro_accession": "3000050", "category_aro_cvterm_id": "36189", "category_aro_name": "tetracycline antibiotic", "category_aro_description": "These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.", "category_aro_class_name": "Drug Class"}}, "$delete": ["35963", "37006", "36298"]}}}, "493": {"$update": {"ARO_category": {"$delete": ["35977", "36981"]}}}, "409": {"$update": {"ARO_category": {"$insert": {"36192": {"category_aro_accession": "3000053", "category_aro_cvterm_id": "36192", "category_aro_name": "peptide antibiotic", "category_aro_description": "Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.", "category_aro_class_name": "Drug Class"}, "48528": {"category_aro_accession": "3009657", "category_aro_cvterm_id": "48528", "category_aro_name": "nonribosomal peptide antibiotics", "category_aro_description": "Nonribosomal peptide antibiotics are peptide natural products synthesized by nonribosomal peptide synthetases (NRPSs), rather than by the ribosome. They often contain non-proteinogenic amino acids and diverse chemical modifications that contribute to their structural and functional diversity.", "category_aro_class_name": "Drug Class"}}, "$delete": ["35947"]}}}, "389": {"$update": {"ARO_category": {"$delete": ["35968", "35986", "36291", "36667", "37011", "37012"]}}}, "497": {"$update": {"ARO_category": {"$delete": ["36026", "35973"]}}}, "498": {"$update": {"ARO_category": {"$delete": ["35954", "35988", "35991", "37003", "37005", "37006", "37010"]}}}, "500": {"$update": {"ARO_category": {"$delete": ["36026", "35973"]}}}, "501": {"$update": {"ARO_category": {"$delete": ["35924"]}}}, "502": {"$update": {"ARO_category": {"$delete": ["35957", "35958"]}}}, "503": {"$update": {"ARO_category": {"$insert": {"46264": {"category_aro_accession": "3007495", "category_aro_cvterm_id": "46264", "category_aro_name": "azole antibiotic", "category_aro_description": "Azoles are a group of antibiotics, particularly antifungals, that target the cytochrome P450 enzyme sterol 14alpha-demethylase, which converts lanosterol to ergosterol. 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In these organisms, these proteins do not bind to the beta-lactam ring and therefore transpeptidase activity continues in the presence of beta-lactams, thereby conferring resistance to these drugs. These proteins are commonly clinically associated with methicillin-resistant Staphylococcus aureus (MRSA).", "category_aro_class_name": "AMR Gene Family"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. 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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.", "category_aro_class_name": "Drug Class"}}}}}, "1384": {"$update": {"ARO_category": {"$delete": ["36026", "35973"]}}}, "1385": {"$update": {"ARO_category": {"$delete": ["36524", "36298"]}}}, "1386": {"$update": {"ARO_category": {"$delete": ["35957"]}}}, "1387": {"$update": {"ARO_category": {"$delete": ["36026", "35973"]}}}, "1388": {"$update": {"ARO_category": {"$delete": ["37247"]}}}, "1390": {"$update": {"ARO_category": {"$insert": {"48501": {"category_aro_accession": "3009640", "category_aro_cvterm_id": "48501", "category_aro_name": "antibiotic efflux regulatory protein", "category_aro_description": "Gene products that regulate efflux of antibiotics from cells.", "category_aro_class_name": "AMR Gene Family"}}, "$delete": ["35954", "35963", "37006", "36298", "36590"]}}}, "1391": {"$update": {"ARO_category": {"$insert": {"46264": {"category_aro_accession": "3007495", "category_aro_cvterm_id": "46264", "category_aro_name": "azole antibiotic", "category_aro_description": "Azoles are a group of antibiotics, particularly antifungals, that target the cytochrome P450 enzyme sterol 14alpha-demethylase, which converts lanosterol to ergosterol. 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However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding/hydrolysis but by proton movement down the transmembrane electrochemical gradient.", "category_aro_class_name": "AMR Gene Family"}, "48501": {"category_aro_accession": "3009640", "category_aro_cvterm_id": "48501", "category_aro_name": "antibiotic efflux regulatory protein", "category_aro_description": "Gene products that regulate efflux of antibiotics from cells.", "category_aro_class_name": "AMR Gene Family"}, "35919": {"category_aro_accession": "0000000", "category_aro_cvterm_id": "35919", "category_aro_name": "macrolide antibiotic", "category_aro_description": "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. 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Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam 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.", "category_aro_class_name": "Drug Class"}, "35939": {"category_aro_accession": "0000020", "category_aro_cvterm_id": "35939", "category_aro_name": "carbapenem", "category_aro_description": "Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem 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.", "category_aro_class_name": "Drug Class"}, "35951": {"category_aro_accession": "0000032", "category_aro_cvterm_id": "35951", "category_aro_name": "cephalosporin", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin 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.", "category_aro_class_name": "Drug Class"}, "36017": {"category_aro_accession": "3000008", "category_aro_cvterm_id": "36017", "category_aro_name": "penicillin beta-lactam", "category_aro_description": "Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like 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.", "category_aro_class_name": "Drug Class"}, "36189": {"category_aro_accession": "3000050", "category_aro_cvterm_id": "36189", "category_aro_name": "tetracycline antibiotic", "category_aro_description": "These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.", "category_aro_class_name": "Drug Class"}, "36192": {"category_aro_accession": "3000053", "category_aro_cvterm_id": "36192", "category_aro_name": "peptide antibiotic", "category_aro_description": "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.", "category_aro_class_name": "Drug Class"}, "36242": {"category_aro_accession": "3000103", "category_aro_cvterm_id": "36242", "category_aro_name": "aminocoumarin antibiotic", "category_aro_description": "Aminocoumarin antibiotics bind DNA gyrase subunit B to inhibit ATP-dependent DNA supercoiling.", "category_aro_class_name": "Drug Class"}, "36310": {"category_aro_accession": "3000171", "category_aro_cvterm_id": "36310", "category_aro_name": "diaminopyrimidine antibiotic", "category_aro_description": "Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.", "category_aro_class_name": "Drug Class"}, "36421": {"category_aro_accession": "3000282", "category_aro_cvterm_id": "36421", "category_aro_name": "sulfonamide antibiotic", "category_aro_description": "Sulfonamides are broad spectrum, synthetic antibiotics that contain the sulfonamide group. Sulfonamides inhibit dihydropteroate synthase, which catalyzes the conversion of p-aminobenzoic acid to dihydropteroic acid as part of the tetrahydrofolic acid biosynthetic pathway. Tetrahydrofolic acid is essential for folate synthesis, a precursor of many nucleotides and amino acids. Many sulfamides are taken with trimethoprim, an inhibitor of dihydrofolate reductase, also disturbing the trihydrofolic acid synthesis pathway.", "category_aro_class_name": "Drug Class"}, "36526": {"category_aro_accession": "3000387", "category_aro_cvterm_id": "36526", "category_aro_name": "phenicol antibiotic", "category_aro_description": "Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.", "category_aro_class_name": "Drug Class"}, "48528": {"category_aro_accession": "3009657", "category_aro_cvterm_id": "48528", "category_aro_name": "nonribosomal peptide antibiotics", "category_aro_description": "Nonribosomal peptide antibiotics are peptide natural products synthesized by nonribosomal peptide synthetases (NRPSs), rather than by the ribosome. 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The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.", "category_aro_class_name": "Drug Class"}}, "$update": {"40661": {"$update": {"category_aro_name": "penicillin-binding protein with mutation conferring resistance to beta-lactam antibiotics"}}}, "$delete": ["35979"]}}}, "3709": {"$update": {"ARO_category": {"$delete": ["35958"]}}}, "3736": {"$update": {"ARO_category": {"$delete": ["40067"]}}}, "3424": {"$update": {"ARO_category": {"$delete": ["36026", "35973"]}}}, "3446": {"$update": {"ARO_category": {"$delete": ["36026", "35973"]}}}, "3475": {"$update": {"ARO_category": {"$delete": ["36026", "35973"]}}}, "3504": {"$update": {"ARO_category": {"$delete": ["36026", "35973"]}}}, "3534": {"$update": {"ARO_category": {"$delete": ["36026", "35973"]}}}, "3742": {"$update": {"ARO_category": {"$delete": ["37140"]}}}, "3746": {"$update": {"model_param": {"$update": {"snp": {"$update": {"ReSeqTB-High": {"$update": {"9820": "N416S"}}}}}}, "ARO_category": {"$delete": ["36308", "36669"]}}}, "3747": {"$update": {"ARO_category": {"$delete": ["36308"]}}}, "3425": {"$update": {"ARO_category": {"$delete": ["36026", "35973"]}}}, "3447": {"$update": {"ARO_category": {"$delete": ["36026", "35973"]}}}, "3476": {"$update": {"ARO_category": {"$delete": ["36026", "35973"]}}}, "3076": {"$update": {"ARO_category": {"$delete": ["36327"]}}}, "3505": {"$update": {"ARO_category": {"$delete": ["36026", "35973"]}}}, "3535": {"$update": {"ARO_category": {"$delete": ["36026", "35973"]}}}, "3712": {"$update": {"ARO_category": {"$delete": ["39997"]}}}, "3738": {"$update": {"ARO_category": {"$delete": ["40067"]}}}, "3426": {"$update": {"ARO_category": {"$delete": ["36026", "35973"]}}}, "3448": {"$update": {"ARO_category": {"$delete": ["36026", "35973"]}}}, "3477": {"$update": {"ARO_category": {"$delete": ["36026", "35973"]}}}, "3506": {"$update": {"ARO_category": {"$delete": ["36026", "35973"]}}}, "3536": {"$update": {"ARO_category": {"$delete": ["36026", "35973"]}}}, "3713": {"$update": {"ARO_category": {"$delete": ["39997"]}}}, "3723": {"$update": {"model_param": {"$update": {"snp": {"$update": {"CRyPTIC-R": {"$update": {"13343": "G48A"}}, "ReSeqTB-High": {"$delete": ["9526"]}}}}, "$delete": ["41345"]}, "ARO_category": {"$delete": ["36659"]}}}, "3128": {"$update": {"ARO_category": {"$insert": {"48528": {"category_aro_accession": "3009657", "category_aro_cvterm_id": "48528", "category_aro_name": "nonribosomal peptide antibiotics", "category_aro_description": "Nonribosomal peptide antibiotics are peptide natural products synthesized by nonribosomal peptide synthetases (NRPSs), rather than by the ribosome. 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Imidazoles include imidazole derivatives clotrimazole, ketoconazole, miconazole, econazole and oxiconazole.", "category_aro_class_name": "Drug Class"}}}}}, "5925": {"$update": {"ARO_category": {"$update": {"40661": {"$update": {"category_aro_name": "penicillin-binding protein with mutation conferring resistance to beta-lactam antibiotics"}}}, "$delete": ["35977", "36689", "36995"]}}}, "209": {"$update": {"ARO_category": {"$delete": ["35922", "35932", "35953", "35966", "35969", "46133"]}}}, "431": {"$update": {"model_name": "Escherichia coli MarR with mutation associated with multidrug resistance", "model_param": {"$update": {"snp": {"$update": {"Curated-R": {"$update": {"3898": "A70T"}}}}}}, "ARO_name": "Escherichia coli MarR with mutation associated with multidrug resistance", "ARO_description": "MarR is a transcriptional regulator and repressor for the expression of marA, itself an activator of the multidrug efflux pump AcrAB. Certain mutations in the marR gene are associated with increased resistance to drugs including tetracycline and ciprofloxacin through increased AcrAB activity.", "ARO_category": {"$insert": {"48501": {"category_aro_accession": "3009640", "category_aro_cvterm_id": "48501", "category_aro_name": "antibiotic efflux regulatory protein", "category_aro_description": "Gene products that regulate efflux of antibiotics from cells.", "category_aro_class_name": "AMR Gene Family"}}, "$delete": ["35949", "35954", "35968", "36308", "36524", "36981", "37084", "37250", "36298", "36590"]}}}, "2306": {"$update": {"model_name": "Escherichia coli AcrR with mutation associated with multidrug resistance", "ARO_name": "Escherichia coli AcrR with mutation associated with multidrug resistance", "ARO_description": "AcrR is a regulator and repressor of the AcrAB-TolC multidrug efflux complex in Escherichia coli. Certain mutations in AcrR are associated with increased tetracycline and fluoroquinolone resistance, among others,  by deregulating the efflux activity of AcrAB-TolC.", "ARO_category": {"$insert": {"48501": {"category_aro_accession": "3009640", "category_aro_cvterm_id": "48501", "category_aro_name": "antibiotic efflux regulatory protein", "category_aro_description": "Gene products that regulate efflux of antibiotics from cells.", "category_aro_class_name": "AMR Gene Family"}}, "$delete": ["35949", "35954", "35968", "35977", "36308", "36524", "36981", "37084", "37250", "36298", "36590"]}}}, "_version": "4.0.2", "_timestamp": "2026-08-11T13:01:48+00:00"}, "$delete": ["2695", "3783", "2215", "2694"]}