{"$update": {"3591": {"$update": {"ARO_category": {"$insert": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms."}}}}}, "212": {"$update": {"ARO_category": {"$delete": ["40471"]}}}, "3595": {"$update": {"ARO_category": {"$insert": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms."}}}}}, "2292": {"$update": {"ARO_category": {"$delete": ["40472"]}}}, "1347": {"$update": {"ARO_description": "OXA-425 is a beta-lactamase found in clinical isolates of Acinetobacter baumannii. It is carbapenem-resistant"}}, "3417": {"$update": {"model_sequences": {"$update": {"sequence": {"5829": {"dna_sequence": {"partial": "0", "sequence": "ATGAAAAAGATAATTTCTCGCTGGCGGCGTGGTGTCTTCGGGCTGCGGGTTGCGCTCGCGGTCGTGTCTCCCATGGTGTTCGCCGTTCCGGCGCATGCGACGGAAGCGGCGGGCGGGGCCGCGGGGACTAAGGCCGCTGCGGTGCACATGAAGGAGCGTGCCGATTGGGGCAAGTTCTTCGATGCGGAAGGTGTTAAGGGAACGATCGTGGTGCTCGACGGACGCACGCAAACGTATCAGGCGTTCGACACGGCGCGCGCCGAGCGGCGGATGTCGCCTGCATCGACGTACAAGATCTTCAACAGCCTGCTGGCGCTCGAGTCGGGCGCCCTCGATAACGAACGCGAGATCATTCCCTGGGACGGCAAGCCGCGACGCGGGAAGTACTGGAACGCGGCGATGGATCTGCGCACGGCGTTTCGCGTGTCGTGTTTGCCGTGCTATCAGGTGGTCTCGCACAAGATTGCGCGTCAGTTTGCACAGAGCAAACTCAATGAGGCCGGGTATGGGAACCACACTATCGGTCGTGCCGCAGACGCCTACTGGGTCGACGACAGCTTGCAGATCTCGGCACGCGAGCAGGTCGATTTCCTGCAACGTCTCGCGCGAGGGACGTTACCGTTCTCTGCACGCTCGCAAGACATCGTGCGTCAGATTTCGATTGTCGAGGCCAATCCTGATTACGTGTTGCATGGCAAGACGGGCTGGTTCGTCGACAAGAAGCCGGACATCGGCTGGTGGGTGGGCTGGATTGAGCGCGACGGCAACATCACGAGCGTAGCGTTGAACATCGATCTGAAGGACGATGCCGATGCGCCCAAGCGCGCCCGTATCGTTCGTGCCGTGCTCAGTAGTTTGCAGTTGATCTGA", "fmax": "24671", "accession": "CEWL01000009.1", "fmin": "23801", "strand": "-"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Pandoraea apista", "NCBI_taxonomy_id": "93218", "NCBI_taxonomy_cvterm_id": "42785"}, "protein_sequence": {"accession": "CFB60580.1", "sequence": "MKKIISRWRRGVFGLRVALAVVSPMVFAVPAHATEAAGGAAGTKAAAVHMKERADWGKFFDAEGVKGTIVVLDGRTQTYQAFDTARAERRMSPASTYKIFNSLLALESGALDNEREIIPWDGKPRRGKYWNAAMDLRTAFRVSCLPCYQVVSHKIARQFAQSKLNEAGYGNHTIGRAADAYWVDDSLQISAREQVDFLQRLARGTLPFSARSQDIVRQISIVEANPDYVLHGKTGWFVDKKPDIGWWVGWIERDGNITSVALNIDLKDDADAPKRARIVRAVLSSLQLI"}}}}}}}, "63": {"$update": {"ARO_category": {"$delete": ["35933", "36461"]}}}, "3270": {"$update": {"model_sequences": {"$update": {"sequence": {"5832": {"dna_sequence": {"partial": "0", "sequence": "ATGAATAAAGAAATTCAATTTTCAATGATTGTAGCGCGTGGTGTAAACGGTGAGATTGGTCAGGACGGCGACTTGCCTTGGCATGTCGAAGGAGTTCGGTTGAAAGAAGACCTCAAACGCTTCAAAGCGATCACTATGGGTAAGACACTCGTCATGGGCAGAAAGACCTTTGAGAGCATCCCCAATGGCCTGCCCGGACGCAACGTCATCGTGCTCACACGCGAGCCTTACGATAAAGCGGATATAACCGAACGTGGAGACGGCACCTTTGTAGCGTGGGGGAATAGCTGCCATCTGTTTGAAGTGGCCGAACACCTGGGCGTTACTGAGATCATCGTGGCGGGCGGTGCTGAAATCTATAATCTGCACAAAGACGTCATTACGAAGGTTTTTGAAACGAAGGTGTTGAGGGCGTATCCTGCAGCGGATACTCACGTAGACGTATTCTGGGAAAGTCCCGGATACGACACTGAAGGCCGACAATGGCGCGTAACGTCCAGAGGCCACATTATCGAAAACGGCAGTTTCACTATCGCGACGACGTATGAGCGATAG", "fmax": "7967", "accession": "AY034138.1", "fmin": "7412", "strand": "-"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Vibrio cholerae MO10", "NCBI_taxonomy_id": "345072", "NCBI_taxonomy_cvterm_id": "39556"}, "protein_sequence": {"accession": "AAK64581.1", "sequence": "MNKEIQFSMIVARGVNGEIGQDGDLPWHVEGVRLKEDLKRFKAITMGKTLVMGRKTFESIPNGLPGRNVIVLTREPYDKADITERGDGTFVAWGNSCHLFEVAEHLGVTEIIVAGGAEIYNLHKDVITKVFETKVLRAYPAADTHVDVFWESPGYDTEGRQWRVTSRGHIIENGSFTIATTYER"}}}}}}}, "991": {"$update": {"model_sequences": {"$update": {"sequence": {"5833": {"dna_sequence": {"partial": "0", "sequence": "ATGACATGGAGAACGACCAGAACACTTTTACAGCCTCAAAAGCTGGACTTCAATGAGTTTGAGATTCTTACTTCCGTAATTGAGGGCGCCCGAATTGTCGGCATTGGCGAGGGCGCTCATTTTGTCGCGGAGTTTTCACTGGCTAGAGCTAGTCTTATCCGCTATTTGGTCGAAAGGCATGAGTTTAATGCGATTGGTTTGGAATGTGGGGCGATTCAGGCATCCCGGTTATCTGAATGGCTCAACTCAACAGCCGGTGCTCATGAACTTGAGCGATTTTCGGATACCCTGACCTTTTCTGTGTATGGCTCAGTGCTGATCTGGCTGAAATCATATCTCCGCGAATCAGGAAGAAAACTGCAGTTAGTCGGAATCGACTTACCCAACACCCTGAACCCAAGGGACGACCTAGCGCAATTGGCCGAAATTATCCAGCTCATCGATCACCTCATGAAACCGCACGTTGATATGTTGACTCACTTGTTGGCGTCCATTGATGGCCAGTCGGCGGTTATTTCATCGGCAAAATGGGGGGAGCTAGAAACGGCTCGGCAGGAGAAAGCTATCTCAGGGGTAACCAGATTGAAGCTCCGCTTGGCGTCGCTTGCCCCCGTCCTGAAAAAACACGTCAACAGCGATTTGTTCCGAAAAGCCTCTGATCGAATAGAGTCGATAGAGTATACGTTGGAAACCTTGCGTATAATGAAAACTTTCTTCGATGGTACCTCTCTTGAGGGAGATACTTCCGTACGTGACTCGTATATGGCGGGCGTAGTAGATGGAATGGTTCGAGCGAATCCGGATGTGAAGATAATTCTGCTGGCGCACAACAATCATCTACAAAAAACTCCAGTCTCCTTTTCAGGCGAGCTTACGGCTGTTCCCATGGGGCAGCACCTCGCAGAGAGGGTGAATTACCGTGCGATTGCATTCACCCATCTTGGACCCACCGTGCCGGAAATGCATTTCCCATCGCCAAAAAGTCCTCTTGGATTCTCTGTTGTGACCACGCCTGCCGATGCAATCCGTGAGGATAGTATGGAACAGTATGTCATCGACGCCTGTGGTACGGAGAATTCATGTCTGACATTGACAGATGCCCCCATGGAAGCAAAGCGAATGCGGTCTCAAAGCGCCTCTGTAGAAACGAAATTGAGCGAGGCATTTGATGCCATCGTCTGTGTTACAAGCGCCGGCAAGGACAGCCTGGTTGCCCTATAG", "fmax": "3950", "accession": "AY183453.1", "fmin": "2729", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Escherichia coli", "NCBI_taxonomy_id": "562", "NCBI_taxonomy_cvterm_id": "35914"}, "protein_sequence": {"accession": "AAO38247.1", "sequence": "MTWRTTRTLLQPQKLDFNEFEILTSVIEGARIVGIGEGAHFVAEFSLARASLIRYLVERHEFNAIGLECGAIQASRLSEWLNSTAGAHELERFSDTLTFSVYGSVLIWLKSYLRESGRKLQLVGIDLPNTLNPRDDLAQLAEIIQLIDHLMKPHVDMLTHLLASIDGQSAVISSAKWGELETARQEKAISGVTRLKLRLASLAPVLKKHVNSDLFRKASDRIESIEYTLETLRIMKTFFDGTSLEGDTSVRDSYMAGVVDGMVRANPDVKIILLAHNNHLQKTPVSFSGELTAVPMGQHLAERVNYRAIAFTHLGPTVPEMHFPSPKSPLGFSVVTTPADAIREDSMEQYVIDACGTENSCLTLTDAPMEAKRMRSQSASVETKLSEAFDAIVCVTSAGKDSLVAL"}}}}}}}, "3558": {"$update": {"ARO_category": {"$insert": {"35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}}}}}, "2785": {"$update": {"ARO_description": "Klebsiella pneumoniae outer membrane porin protein. Is preferentially detected in porin-deficient strains. Functional characterization of this new porin revealed a narrower pore than those of porins OmpK35 and OmpK36, which did not allow penetration by certain beta-lactams. Also, when a resistant strain expresses porin OmpK37 is less susceptible to cefotaxime and cefoxitin than when it is expressing either OmpK36 or OmpK35."}}, "2397": {"$update": {"ARO_description": "A gene that produces the protein lipid A 4'-phosphatase"}}, "3575": {"$update": {"ARO_category": {"$insert": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms."}}}}}, "3574": {"$update": {"ARO_category": {"$insert": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms."}}}}}, "3576": {"$update": {"ARO_category": {"$insert": {"35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}}}}}, "3559": {"$update": {"ARO_category": {"$insert": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms."}}}}}, "1549": {"$update": {"model_sequences": {"$update": {"sequence": {"5828": {"dna_sequence": {"partial": "1", "sequence": "ATGAACAAAAATATAAAATATTCTCAAAACTTTTTAACGAGTGAAAAAGTACTCAACCAAATAATAAAACAATTGAATTTAAAAGAAACCGATACCGTTTACGAAATTGGAACAGGTAAAGGGCATTTAACGACGAAACTGGCTAAAATAAGTAAACAGGTAACGTCTATTGAATTAGACAGTCATCTATTCAACTTATCGTCAGAAAAATTAAAACTGAATACTCGTGTCACTTTAATTCACCAAGATATTCTACAGTTTCAATTCCCTAACAAACAGAGGTATAAAATTGTTGGGAGTATTCCTTACAATTTAAGCACACAAATTATTAAAAAAGTGGTTTTTGAAAGCCGTGCGTCTGACATCTATCTGATTGTTGAAGAAGGATTCTACAAGCGTACCTTGGATATTCACCGAACACTAGGGTTGCTCTTGCACACTCAAGTCTCGATTCAGCAATTGCTTAAGCTGCCAGCGGAATGCTTTCATCCTAAACCAAAAGTAAACAGTGTCTTAATAAAACTTACCCGCCATACCACAGATGTTCCAGATAAATATTGGAAGCTATATACGTACTTTGTTTCAAAATGGGTCAATCGAGAATATCGTCAACTGTTTACTAAAAATCAGTTTCATCAAGCAATGAAACACGCCAAAGTAAACAATTTAAGTACCATTACTTATGAGCAAGTATTGTCTATTTTTAATAGTTATCTATTATTTAACGGGAGGAAATTAATTCTATGA", "fmax": "2878", "accession": "AF242872.1", "fmin": "2131", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Enterococcus faecium", "NCBI_taxonomy_id": "1352", "NCBI_taxonomy_cvterm_id": "36779"}, "protein_sequence": {"accession": "AAF86219.1", "sequence": "MNKNIKYSQNFLTSEKVLNQIIKQLNLKETDTVYEIGTGKGHLTTKLAKISKQVTSIELDSHLFNLSSEKLKLNTRVTLIHQDILQFQFPNKQRYKIVGSIPYNLSTQIIKKVVFESRASDIYLIVEEGFYKRTLDIHRTLGLLLHTQVSIQQLLKLPAECFHPKPKVNSVLIKLTRHTTDVPDKYWKLYTYFVSKWVNREYRQLFTKNQFHQAMKHAKVNNLSTITYEQVLSIFNSYLLFNGRKLIL"}}}}}}}, "_timestamp": "2019-09-18T12:47:48+00:00", "3580": {"$update": {"ARO_category": {"$insert": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms."}}}}}, "3582": {"$update": {"ARO_category": {"$insert": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms."}}}}}, "3583": {"$update": {"ARO_category": {"$insert": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms."}}}}}, "2914": {"$update": {"ARO_description": "Bifidobacterium are antibiotic resistant probiotics are prescribed to upkeep the population beneficial bacteria in the gut microbiome. However, horizontal gene transfer among gut microbes could create harmful antibiotic-resistant pathogenic bacteria, such as Mycobacterium tuberculosis. Lokesh et al. analyzed Bifidobacterium antitubercular drug resistance and mutations in rpoB. They found that B. animalis, B. longum and B. adolescentis showed considerable resistance to pyrazinamide, isoniazid, and streptomycin, while B. adolescentis had mutations both in the rifampicin (RIF) pocket and in regions outside the pockets, and also showed considerable resistance to RIF."}}, "900": {"$update": {"model_sequences": {"$update": {"sequence": {"5826": {"dna_sequence": {"partial": "0", "sequence": "ATGAAATCTAACAATGCGCTCATCGTCATCCTCGGCACCGTCACCCTGGATGCTGTAGGCATAGGCTTGGTTATGCCGGTACTGCCGGGCCTCTTGCGGGATATCGTCCATTCCGACAGCATCGCCAGTCACTATGGCGTGCTGCTAGCGCTATATGCGTTGATGCAATTTCTATGCGCACCCGTTCTCGGAGCACTGTCCGACCGCTTTGGCCGCCGCCCAGTCCTGCTCGCTTCGCTACTTGGAGCCACTATCGACTACGCGATCATGGCGACCACACCCGTCCTGTGGATCCTCTACGCCGGACGCATCGTGGCCGGCATCACCGGCGCCACAGGTGCGGTTGCTGGCGCCTATATCGCCGACATCACCGATGGGGAAGATCGGGCTCGCCACTTCGGGCTCATGAGCGCTTGTTTCGGCGTGGGTATGGTGGCAGGCCCCGTGGCCGGGGGACTGTTGGGCGCCATCTCCTTGCATGCACCATTCCTTGCGGCGGCGGTGCTCAACGGCCTCAACCTACTACTGGGCTGCTTCCTAATGCAGGAGTCGCATAAGGGAGAGCGTCGACCGATGCCCTTGAGAGCCTTCAACCCAGTCAGCTCCTTCCGGTGGGCGCGGGGCATGACTATCGTCGCCGCACTTATGACTGTCTTCTTTATCATGCAACTCGTAGGACAGGTGCCGGCAGCGCTCTGGGTCATTTTCGGCGAGGACCGCTTTCGCTGGAGCGCGACGATGATCGGCCTGTCGCTTGCGGTATTCGGAATCTTGCACGCCCTCGCTCAAGCCTTCGTCACTGGTCCCGCCACCAAACGTTTCGGCGAGAAGCAGGCCATTATCGCCGGCATGGCGGCCGACGCGCTGGGCTACGTCTTGCTGGCGTTCGCGACGCGAGGCTGGATGGCCTTCCCCATTATGATTCTTCTCGCTTCCGGCGGCATCGGGATGCCCGCGTTGCAGGCCATGCTGTCCAGGCAGGTAGATGACGACCATCAGGGACAGCTTCAAGGATCGCTCGCGGCTCTTACCAGCCTAACTTCGATCATTGGACCGCTGATCGTCACGGCGATTTATGCCGCCTCGGCGAGCACATGGAACGGGTTGGCATGGATTGTAGGCGCCGCCCTATACCTTGTCTGCCTCCCCGCGTTGCGTCGCGGTGCATGGAGCCGGGCCACCTCGACCTGA", "fmax": "5175", "accession": "AY043299.1", "fmin": "3984", "strand": "-"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Aeromonas salmonicida", "NCBI_taxonomy_id": "645", "NCBI_taxonomy_cvterm_id": "36795"}, "protein_sequence": {"accession": "AAK97755.1", "sequence": "MKSNNALIVILGTVTLDAVGIGLVMPVLPGLLRDIVHSDSIASHYGVLLALYALMQFLCAPVLGALSDRFGRRPVLLASLLGATIDYAIMATTPVLWILYAGRIVAGITGATGAVAGAYIADITDGEDRARHFGLMSACFGVGMVAGPVAGGLLGAISLHAPFLAAAVLNGLNLLLGCFLMQESHKGERRPMPLRAFNPVSSFRWARGMTIVAALMTVFFIMQLVGQVPAALWVIFGEDRFRWSATMIGLSLAVFGILHALAQAFVTGPATKRFGEKQAIIAGMAADALGYVLLAFATRGWMAFPIMILLASGGIGMPALQAMLSRQVDDDHQGQLQGSLAALTSLTSIIGPLIVTAIYAASASTWNGLAWIVGAALYLVCLPALRRGAWSRATST"}}}}}}}, "1135": {"$update": {"model_sequences": {"$update": {"sequence": {"$update": {"3681": {"$update": {"NCBI_taxonomy": {"$update": {"NCBI_taxonomy_name": "Staphylococcus aureus subsp. aureus RN4220"}}}}}}}}}}, "3402": {"$update": {"model_sequences": {"$update": {"sequence": {"5831": {"dna_sequence": {"partial": "0", "sequence": "ATGAGCAATAAAGAAAAACAAATGAATTTACTTAGTGATAAGAACGTTGCAATAATTGGTGGTGGACCCGTTGGACTGACTATGGCAAAATTATTACAGCAAAACGGCATAGACGTTTCAGTTTACGAAAGAGACAACGACCGAGAGGCAAGAATTTTTGGTGGAACCCTTGACCTACACAAAGGTTCAGGTCAGGAAGCAATGAAAAAAGCGGGATTGTTACAAACTTATTATGACTTAGCCTTACCAATGGGTGTAAATATTGCTGATGAAAAAGGCAATATTTTATCCACAAAAAATGTAAAGCCCGAAAATCGATTTGACAATCCTGAAATAAACAGAAATGACTTAAGGGCTATCTTGTTGAATAGTTTAGAAAACGACACGGTTATTTGGGATAGAAAACTTGTTATGCTTGAACCTGGTAAGAAGAAGTGGACACTAACTTTTGAGAATAAACCGAGTGAAACAGCAGATCTGGTTATTATTGCCAATGGTGGAATGTCTAAAGTAAGAAAATTTGTTACCGACACGGAAGTTGAAGAAACAGGTACTTTCAATATACAAGCCGATATTCATCATCCAGAGGTGAACTGTCCTGGATTTTTTCAGCTATGCAATGGAAACCGGCTAATGGCTGCTCATCAAGGTAATTTATTATTTGCGAATCCTAATAATAATGGTGCATTGCATTTTGGAATAAGTTTTAAAACACCTGATGAATGGAAAAACCAAACGCAGGTAGATTTTCAAAACAGAAATAGTGTCGTTGATTTTCTTCTGAAAGAATTTTCCGATTGGGACGAACGCTACAAAGAACTGATTCGTGTGACATCATCTTTTGTAGGGTTAGCGACACGAATATTTCCCTTAGGTAAGTCTTGGAAAAGTAAGCGTCCATTACCCATAACGATGATTGGAGATGCTGCTCATTTGATGCCTCCTTTTGCAGGACAAGGCGTAAACAGCGGGTTGATGGATGCCTTGATATTGTCGGATAATCTGACCAATGGGAAATTTAACAGCATTGAAGAGGCTATTGAAAATTATGAACAGCAAATGTTTATCTATGGCAAAGAAGCACAAGAAGAATCAACTCAAAACGAAATTGAAATGTTTAAACCCGACTTTACGTTTCAGCAATTGTTAAATGTATAA", "fmax": "1482", "accession": "MK134376.1", "fmin": "324", "strand": "-"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Escherichia coli", "NCBI_taxonomy_id": "562", "NCBI_taxonomy_cvterm_id": "35914"}, "protein_sequence": {"accession": "QBQ69719.1", "sequence": "MSNKEKQMNLLSDKNVAIIGGGPVGLTMAKLLQQNGIDVSVYERDNDREARIFGGTLDLHKGSGQEAMKKAGLLQTYYDLALPMGVNIADEKGNILSTKNVKPENRFDNPEINRNDLRAILLNSLENDTVIWDRKLVMLEPGKKKWTLTFENKPSETADLVIIANGGMSKVRKFVTDTEVEETGTFNIQADIHHPEVNCPGFFQLCNGNRLMAAHQGNLLFANPNNNGALHFGISFKTPDEWKNQTQVDFQNRNSVVDFLLKEFSDWDERYKELIRVTSSFVGLATRIFPLGKSWKSKRPLPITMIGDAAHLMPPFAGQGVNSGLMDALILSDNLTNGKFNSIEEAIENYEQQMFIYGKEAQEESTQNEIEMFKPDFTFQQLLNV"}}}}}}}, "660": {"$update": {"ARO_category": {"$delete": ["40471"]}}}, "3562": {"$update": {"ARO_category": {"$insert": {"35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}}}}}, "3563": {"$update": {"ARO_category": {"$insert": {"35939": {"category_aro_name": "carbapenem", "category_aro_cvterm_id": "35939", "category_aro_accession": "0000020", "category_aro_class_name": "Drug Class", "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."}}}}}, "3560": {"$update": {"ARO_category": {"$insert": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms."}}}}}, "3561": {"$update": {"ARO_category": {"$insert": {"35939": {"category_aro_name": "carbapenem", "category_aro_cvterm_id": "35939", "category_aro_accession": "0000020", "category_aro_class_name": "Drug Class", "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."}}}}}, "3567": {"$update": {"ARO_category": {"$insert": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms."}}}}}, "2215": {"$update": {"ARO_category": {"$delete": ["37010", "39876", "35988", "37007", "35954", "37142", "40338"]}}}, "2041": {"$update": {"ARO_description": "OXA-424 is a beta-lactamase found in clinical isolates of Acinetobacter baumannii found in China. It is carbapenem resistant."}}, "2230": {"$update": {"model_sequences": {"$update": {"sequence": {"5834": {"dna_sequence": {"partial": "0", "sequence": "ATGCGTTATCTTCTTTCCTTTTTACTTTGTTTATCTGCCTTTGCCTCTTTCGCGCAAAATCCAAAAATAAAAATCAAACATTTAACTGGCGATCTTTATGTTTACACCACATACAATACCTACAAAGGCGCTTTAACAGATGCAAATGCGGTTTACCTGGTTACCAATAAAGGTGTTGTAGTAATCGATGCCCCTTGGGATGCTACGCAGTTCCAGCCCTTTTTAGACTCTATTCAGACCAAACATCACCAAAAAGTAGTGCTGGCCATTGCCACACATTCGCATGGCGACCGCGCAGGCGGTTTAGCGTTCTTTAAAAGTAAGGGCATAAAAACCTATACCAATAAATTAACCGACGAAATTCTGAAAACTAATAAAGAGCCACGCGCAGCCTACACCTTTACCAACGACACTACTTTTACAGTGGGACAATATAAAATAAACACCTACTATGCCGGCAAGGGGCATACAAAGGATAATCTGGTAGTTTGGTTTCCAAAAGACAAAGTTTTATTCGGTGGCTGCCTGATTAAAAGCATCGAAGCCAATGATTTGGGCTATATTGGAGAATCCGATTTAGCCGCATGGCCAAAAAGCATCGAAAAGTTAAAACAGAAATATCCTGATACCAAAATTGTTATTACCGGACACGCTGCCTGGGGAAACAGGGAATCTCTAGACCATACCCTAAAGCTATTGAGGGAGAAAAAGTAG", "fmax": "2974", "accession": "KP109679", "fmin": "2260", "strand": "-"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Pedobacter sp. Stok-3", "NCBI_taxonomy_id": "1620223", "NCBI_taxonomy_cvterm_id": "40285"}, "protein_sequence": {"accession": "AJP77076", "sequence": "MRYLLSFLLCLSAFASFAQNPKIKIKHLTGDLYVYTTYNTYKGALTDANAVYLVTNKGVVVIDAPWDATQFQPFLDSIQTKHHQKVVLAIATHSHGDRAGGLAFFKSKGIKTYTNKLTDEILKTNKEPRAAYTFTNDTTFTVGQYKINTYYAGKGHTKDNLVVWFPKDKVLFGGCLIKSIEANDLGYIGESDLAAWPKSIEKLKQKYPDTKIVITGHAAWGNRESLDHTLKLLREKK"}}}}}}}, "3568": {"$update": {"ARO_category": {"$insert": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms."}}}}}, "2235": {"$update": {"model_sequences": {"$update": {"sequence": {"5827": {"dna_sequence": {"partial": "0", "sequence": "ATGCGCCCCCTGATACTGCTCGCATCCGCGCTCGCCATGACAGCCCCATCCGGCGCCCTCGCCCAATCGGCCGAGCAGCGCGCGAAATGGAACGGGCCGCGCGAGCCATTCCGCATCACCGGCAATCTCTATTATGTCGGCACCAGCGGGCTTTCGGCCTATCTGATCGCCGGGCCGCGCGGCCATGTGCTGATCGACGGCGCTCTGCCGGAAAGCGCGCCGCTGATCGCCGCGAACATCCGCAAACTGGGCTTCAAACTGTCCGATGTGAAATATCTGCTCAGCAACCATTCGCATGTCGATCACGCCGGTGGACTGGCCGAACTCAAGCGGCTGACCGGCGCGCAAATGGTCGCAAACGTTGCGGACAAGCCCGATCTCGAAGCAGGTACCACCATCGGCCGCACCGATATCGCGGACTTTCCGGCAGTGAAGGTCGATCGTGTGATCGGCGACGGCGACCGGCTGACGCTCGGCCCGATCGCGCTCGTCGCCATCCTGACACCCGGCCATACAAAAGGCGCGACGAGCTGGACGACCCGCATTGGCAGCAAGAATGTGATCTTCACATCGAGTATCAGTGTCGCCGGCCAAAATCTTATCAATAATATAAATTATCCGAACGCCGCCGCCGATTTCCGTGCCAGCTTTGCGAAACTCCGCGCGTTGAAGGCAGATATCTTCCTGAGCTTCCACGCCGAGGCTTTCGCGCTCGATGAAAAACGCGCCAGGGCGCAGGCGGGTGCCACCGACGCCTTTGTCGATCCGAACGAATTGTCACGCCAGGTCGATCTGGCGGAGAAGGCTTTCGATGCGACGCTGGCGAAGCAGCAAGCGGCGAATGCGGATCGGCGCTGA", "fmax": "2112", "accession": "KP109680", "fmin": "1254", "strand": "-"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Sphingomonas sp. ALS-13", "NCBI_taxonomy_id": "1620224", "NCBI_taxonomy_cvterm_id": "40286"}, "protein_sequence": {"accession": "AJP77080", "sequence": "MRPLILLASALAMTAPSGALAQSAEQRAKWNGPREPFRITGNLYYVGTSGLSAYLIAGPRGHVLIDGALPESAPLIAANIRKLGFKLSDVKYLLSNHSHVDHAGGLAELKRLTGAQMVANVADKPDLEAGTTIGRTDIADFPAVKVDRVIGDGDRLTLGPIALVAILTPGHTKGATSWTTRIGSKNVIFTSSISVAGQNLINNINYPNAAADFRASFAKLRALKADIFLSFHAEAFALDEKRARAQAGATDAFVDPNELSRQVDLAEKAFDATLAKQQAANADRR"}}}}}}}, "_version": "3.0.5", "2310": {"$update": {"ARO_category": {"$delete": ["40497"]}}}, "3584": {"$update": {"ARO_category": {"$insert": {"35939": {"category_aro_name": "carbapenem", "category_aro_cvterm_id": "35939", "category_aro_accession": "0000020", "category_aro_class_name": "Drug Class", "category_aro_description": "Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "category_aro_description": "Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms."}}}}}, "3415": {"$update": {"model_sequences": {"$update": {"sequence": {"5825": {"dna_sequence": {"partial": "0", "sequence": "ATGAATACGATAATTTCTCGCCGGTGGCGTGCCGGCCTGTGGCGGCGGCTGGTCGGCGCGGTCGTCTTGCCCGCAACGCTCGCCGCCACCCCTGCGGCCTATGCGGCCGACGTGCCGAAAGCCGCGCCGGGGCGCATCACCGAGCGCGCCGACTGGGGCAAGCTGTTCACCGCGGAGGGCGTGAAGGGCACGATCGTGGTGCTCGACGCACGCACGCAAACCTATCAGGCCTACGACGCCGCACGTGCCGAGAAGCGCATGTCGCCGGCGTCGACTTACAAGATATTCAACAGCCTGCTGGCGCTCGACTCCGGGGCGCTGGACAACGAACGCGCGATCATTCCCTGGGATGGCAAGCCGCGACGCATCAAGAACTGGAACGCGGCGATGGACCTGAGGACCGCGTTTCGCGTGTCATGCCTGCCCTGCTATCAGGTCGTCTCGCACAAGATCGGGCGCCGGTACGCGCAGGCGAAGCTGAACGAGGTCGGGTATGGCAACCGCACCATTGGCGGCGCGCCGGACGCCTATTGGGTCGACGACAGTCTGCAGATTTCGGCGCGTGAGCAGGTGGACTTCCTGCAGCGTCTCGCGCGTGGCACGTTGCCGTTCTCTGCGCGCTCGCAGGACATCGTGCGCCAGATGTCGATCGTCGAAGCCACGCCGGACTATGTGCTTCACGGCAAGACGGGCTGGTTCGTCGACAAGAAGCCCGATATCGGCTGGTGGGTAGGGTGGATCGAGCGCGACGGCAACATCGCCAGCGTCGCGATCAACATCGACATGCTGTCGGAGGCGGACGCCCCGAAACGGGCACGCATCGTGAAGTCGGTGCTGAAGGACCTGAAGCTGATCTGA", "fmax": "1910080", "accession": "UGSG01000001.1", "fmin": "1909222", "strand": "-"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Pandoraea pnomenusa", "NCBI_taxonomy_id": "93220", "NCBI_taxonomy_cvterm_id": "36932"}, "protein_sequence": {"accession": "SUA76968.1", "sequence": "MNTIISRRWRAGLWRRLVGAVVLPATLAATPAAYAADVPKAAPGRITERADWGKLFTAEGVKGTIVVLDARTQTYQAYDAARAEKRMSPASTYKIFNSLLALDSGALDNERAIIPWDGKPRRIKNWNAAMDLRTAFRVSCLPCYQVVSHKIGRRYAQAKLNEVGYGNRTIGGAPDAYWVDDSLQISAREQVDFLQRLARGTLPFSARSQDIVRQMSIVEATPDYVLHGKTGWFVDKKPDIGWWVGWIERDGNIASVAINIDMLSEADAPKRARIVKSVLKDLKLI"}}}}}}}, "1450": {"$update": {"ARO_category": {"$delete": ["40471"]}}}, "2753": {"$update": {"ARO_description": "Shotgun cloning of beta-lactam resistant P. aeruginosa NRZ-03096 yielded a clone producing a novel subclass B1 enzyme with only 74.3% identity to the next nearest relative, KHM-1. The novel MBL was named HMB-1 (for Hamburg MBL). HMB-1 gene was chromosomally located as part of a Tn 3 family transposon that was named Tn 6345, where expression of bla HMB-1 in E. coli TOP10 led to increased resistance to beta-lactams."}}, "2083": {"$update": {"ARO_category": {"$delete": ["40471"]}}}, "2104": {"$update": {"ARO_category": {"$delete": ["40471"]}}}}, "$delete": ["3414", "2898", "737"], "$insert": {"3613": {"model_id": "3613", "ARO_accession": "3004819", "model_param": {"blastp_bit_score": {"param_value": "590", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with 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. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "HERA-4 is a class A beta-lactamase found in Escherichia hermannii.", "model_sequences": {"sequence": {"5811": {"dna_sequence": {"partial": "0", "sequence": "ATGAAAAAAATCACCCCGCTCTTTGTCATCGCATTTCTGACTCTGATCGCGTTACTGGCCCCGGCGCAGGCCTCCGTCACGCCAGATATGACGGACTTTTTACGCCAGCAGGAGCAACGGCTTCACGCCAGAATTGGCATGGCGGTTGTCAACGCGCAAGGCGAAACGGTGTTCGGTTATCGGCAGGACGAGCGTTTCCCGCTGACCAGCACCTTTAAAACCCTGGCCTGCGCCGCGTTGCTTGAGCGGTTGCAGAAAAACGGCGGTTCGCTGGATGAACAGGTGACTATTCCGCCAGACGCCTTGCTGGACTATGCGCCAGTGACTAAAAACTACCTCGCCCCTGCCACCATCTCTTTACGCATGCTGTGCGCGGCGGCGGTGAGCTACAGCGACAACACGGCGGGCAACCGCATTCTGACTTACCTTGCCGGCCCTGATGCCGTCACGCAGTTTATGCGCGGGATCGGCGACCATGTGACCCGTCTGGATCGAACGGAGCCCACGCTGAATGAAGCCACGCCAGGCGATGCGCGCGATACCTCTTCGCCGCAGAAGATGGCGGCAGGGCTGCAAAAAATCCTCACCTCCCCTCCCCTGATATCGGCTAACCGGGCGACGCTGGCGCAGTGGATGCGTGACGATAAAGTGGGAGATGCGCTGCTACGCGCCGCGCTGCCGAAAGGCTGGGCAATTGCCGATAAAACCGGGGCGGGCGGCTACGGCTCGCGGGCGATTATCGCGGCGGTCTATCCGCCGGAACGCCCGCCGTTTTATGTCGCGATTTTTATTACGCAAACGGAAGCCTCGATGAAAATGGCAAATGAAACCACTGCTGAAATCGGCAAGCAGTTGTTTGCCGGGCAGCCCTGA", "fmax": "873", "accession": "AJ536088.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Atlantibacter hermannii", "NCBI_taxonomy_id": "565", "NCBI_taxonomy_cvterm_id": "41643"}, "protein_sequence": {"accession": "CAD60968.1", "sequence": "MKKITPLFVIAFLTLIALLAPAQASVTPDMTDFLRQQEQRLHARIGMAVVNAQGETVFGYRQDERFPLTSTFKTLACAALLERLQKNGGSLDEQVTIPPDALLDYAPVTKNYLAPATISLRMLCAAAVSYSDNTAGNRILTYLAGPDAVTQFMRGIGDHVTRLDRTEPTLNEATPGDARDTSSPQKMAAGLQKILTSPPLISANRATLAQWMRDDKVGDALLRAALPKGWAIADKTGAGGYGSRAIIAAVYPPERPPFYVAIFITQTEASMKMANETTAEIGKQLFAGQP"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms."}, "41641": {"category_aro_name": "HERA beta-lactamase", "category_aro_cvterm_id": "41641", "category_aro_accession": "3004447", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "A class A beta-lactamase family shown to hydrolyze penicillin but without cephalosporinase activity."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}}, "ARO_name": "HERA-4", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "42949", "model_name": "HERA-4", "model_type_id": "40292"}, "3614": {"model_id": "3614", "ARO_accession": "3004820", "model_param": {"blastp_bit_score": {"param_value": "590", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with 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. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "HERA-5 is a class A beta-lactamase found in Escherichia hermannii.", "model_sequences": {"sequence": {"5812": {"dna_sequence": {"partial": "0", "sequence": "ATGAAAAAAATCACCCCGCTCTTTGCCATCGCATTTCTGACCCTGATCGCGTTACTGGCCCCGGCGCAGGCCTCCGTCACGCCAGATATGACGGACTTTTTACGCCAGCAGGAGCAACGGCTTCACGCCAGAATTGGCATGGCGGTTGTCAACGCGCAAGGCGAAACGGTGTTCGGTTATCGGCAGGACGAGCGTTTCCCGCTGACCAGCACCTTTAAAACCCTGGCCTGCGCCGCGTTGCTTGAGCGATTGCAGAAAAACGGCGGTTCGCTGGATGAACAGGTGACTATTCCGCCAGACGCCTTGCTGGACTATGCGCCAGTGACTAAAAACTACCTCGCCCCTGCCACCATCTCCTTACGCATGTTGTGCGCAGCGGCGGTGAGCTACAGCGACAACACGGCGGGCAACCGCATTCTGACTTACCTTGGCGGCCCGGATGCCGTCACGCAGTTTATGCGCGGGATCGGCGAACATGTGACCCGTCTGGATCGAACGGAGCCCACGCTGAATGAAGCCACGCCAGGCGATGCGCGCGATACCTCTTCGCCGCAGAAGATGGCGGCAGGGCTGCAAAAAATCCTCACCGCCCCTCCCCTGACACCGGCTAACCGGGCGACGCTGGCGCAGTGGATGCGTGACGATAAAGTGGGAGATGCGCTGCTACGCGCCGCGCTGCCGAAAGGCTGGGCAATTGCCGATAAAACCGGGGCGGGCGGCTACGGCTCGCGGGCGATTATCGCGGCGGTCTATCCGCCGGAACGCCCGCCGTTTTATGTCGCGATTTTTATTACGCAAACGGAAGCCTCGATGAAAATGGCAAATGAAACCATTGCTGAAATCGGCAAGCAGTTGTTTGCCGGGCAGCCCTGA", "fmax": "873", "accession": "AJ536089.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Atlantibacter hermannii", "NCBI_taxonomy_id": "565", "NCBI_taxonomy_cvterm_id": "41643"}, "protein_sequence": {"accession": "CAD60969.1", "sequence": "MKKITPLFAIAFLTLIALLAPAQASVTPDMTDFLRQQEQRLHARIGMAVVNAQGETVFGYRQDERFPLTSTFKTLACAALLERLQKNGGSLDEQVTIPPDALLDYAPVTKNYLAPATISLRMLCAAAVSYSDNTAGNRILTYLGGPDAVTQFMRGIGEHVTRLDRTEPTLNEATPGDARDTSSPQKMAAGLQKILTAPPLTPANRATLAQWMRDDKVGDALLRAALPKGWAIADKTGAGGYGSRAIIAAVYPPERPPFYVAIFITQTEASMKMANETIAEIGKQLFAGQP"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms."}, "41641": {"category_aro_name": "HERA beta-lactamase", "category_aro_cvterm_id": "41641", "category_aro_accession": "3004447", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "A class A beta-lactamase family shown to hydrolyze penicillin but without cephalosporinase activity."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}}, "ARO_name": "HERA-5", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "42950", "model_name": "HERA-5", "model_type_id": "40292"}, "3615": {"model_id": "3615", "ARO_accession": "3004821", "model_param": {"blastp_bit_score": {"param_value": "588", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with 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. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "HERA-6 is a class A beta-lactamase found in Escherichia hermannii.", "model_sequences": {"sequence": {"5813": {"dna_sequence": {"partial": "0", "sequence": "ATGAAAAAAATCACCCCGCTCTTCGCCATCGCATTTCTAACCCTGATCGCGTTACTGGCTCCGGCACAGGCCTCCGTCACGCCAGATATGACGGACTTTTTACGCCAGCAGGAGCAACGGCTTCACGCCAGAATTGGCATGGCGGTTGTCAACGCGCAAGGCGAAACGGTGTTCGGTTATCGGCAGGACGAGCGTTTCCCGCTGACCAGCACCTTTAAAACCCTGGCCTGCGCCGCGTTGCTTGAGCGGTTGCAGAAAAACGGCGGTTCGCTGGATGAACAGGTGACTATTCCGCCAGACGCCTTGCTGGACTATGCGCCAGTGACTAAAAACTACCTCGCCCCTGCCACCATCTCCTTACGCATGTTGTGCGCAGCGGCGGTGAGCTACAGCGACAACACGGCGGGCAACCGCATTCTGACTTACCTTGGCGGCCCGGATGCCGTCACGCAGTTTATGCGCGGGATCGGCGACCATGTGACCCGTCTGGATCGAACGGAGCCCACGCTGAATGAAGCCACGCCAGGCGATGCGCGCGATACCTCTTCGCCGCAGAAGATGGCGGCAGGGCTGCAAAAAATCCTCACCGCCCCGCCCCTGACGCCGGCTAACCGGGCGACGCTGGCGCAATGGATGCGTGACGATAAAGTGGGAGATGCGCTGCTACGCGCCGCGCTGCCGAAAGGCTGGGCGATTGCCGATAAAACCGGGGCGGGCGGCTACGGCTCGCGGGCGATTATCGCGGCGGTCTATCCGCCGGAACGCCCGCCGTTTTATGTCGCGATTTTTATTACGCAAACCGAAGCCTCAATGAAAATGGCAAATGAAGCCATTGCTGCAATCGGCAAGCAGTTGTTTGCCGGGCAGCCCTGA", "fmax": "873", "accession": "AJ536090.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Atlantibacter hermannii", "NCBI_taxonomy_id": "565", "NCBI_taxonomy_cvterm_id": "41643"}, "protein_sequence": {"accession": "CAD60970.1", "sequence": "MKKITPLFAIAFLTLIALLAPAQASVTPDMTDFLRQQEQRLHARIGMAVVNAQGETVFGYRQDERFPLTSTFKTLACAALLERLQKNGGSLDEQVTIPPDALLDYAPVTKNYLAPATISLRMLCAAAVSYSDNTAGNRILTYLGGPDAVTQFMRGIGDHVTRLDRTEPTLNEATPGDARDTSSPQKMAAGLQKILTAPPLTPANRATLAQWMRDDKVGDALLRAALPKGWAIADKTGAGGYGSRAIIAAVYPPERPPFYVAIFITQTEASMKMANEAIAAIGKQLFAGQP"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms."}, "41641": {"category_aro_name": "HERA beta-lactamase", "category_aro_cvterm_id": "41641", "category_aro_accession": "3004447", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "A class A beta-lactamase family shown to hydrolyze penicillin but without cephalosporinase activity."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}}, "ARO_name": "HERA-6", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "42951", "model_name": "HERA-6", "model_type_id": "40292"}, "3616": {"model_id": "3616", "ARO_accession": "3004822", "model_param": {"blastp_bit_score": {"param_value": "580", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with 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. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "HERA-8 is a class A beta-lactamase found in Escherichia hermannii.", "model_sequences": {"sequence": {"5814": {"dna_sequence": {"partial": "0", "sequence": "ATGAAAAAAATCACCCCGCTCTTTGCCATCGCATTTCTGACCCTGATCGCGTTACTGGCTCCGGCACAGGCCTCCGTCACGCCAGACATGACGGACTTTTTACGCCAGCAGGAGCAACGGCTTCACGCCAGAATTGGCATGGCGGTTGTCAACGCGCAAGGCGAAACGGTGTTCGGTTATCGGCAGGACGAGCGTTTCCCGCTGACCAGCACCTTTAAAACCCTGGCCTGCGCCGCGTTGCTTGAGCGGTTGCAGAAAAACGGCGGTTCGCTGGATGAACAGGTGACTATTCCGCCAGACGCCTTGCTGGACTATGCGCCAGTGACTAAAAACTACCTCGCCCCTGCCACCATCTCTTTACGCATGCTGTGCGCGGCGGCGGTGAGCTACAGCGACAACACGGCGGGCAACCGCATTCTGACTTACCTTGGCGGCCCGGATGCCGTCACGCAGTTTATGCGCGGGATCGGCGACCCTGTGACCCGTCTGGATCGGACGGAGCCCACGCTGAATGAAGCCACGCCAGGCGATGCGCGCGATACCTCTTCGCCGCAGAAGATGGCGGCAGGGCTGCAAAAAATCCTCACCGCCCCTCCCCTGACGCCGGCTAACCGGGCGGTGCTGGCGCAGTGGATGCGTGACGATAAAGTGGGAGATGCGCTGCTACGCGCCGCGCTGCCGAAAGGCTGGGCAATTGCCGATAAAACCGGGGCGGGCGGCTACGGCTCGCGGGCGATTATCGCGGCGGTCTATCCGCCGGAACGCCCGCCGTTTTATGTCGCGATTTTTATTACGCAAACGGAAGCCTCAATGAAAATGGCAAATGAAGCCATTCCCGCAATCGGCAAGCAGTTGTTTGCCGGGCAGCCCTGA", "fmax": "873", "accession": "AJ536092.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Atlantibacter hermannii", "NCBI_taxonomy_id": "565", "NCBI_taxonomy_cvterm_id": "41643"}, "protein_sequence": {"accession": "CAD60972.1", "sequence": "MKKITPLFAIAFLTLIALLAPAQASVTPDMTDFLRQQEQRLHARIGMAVVNAQGETVFGYRQDERFPLTSTFKTLACAALLERLQKNGGSLDEQVTIPPDALLDYAPVTKNYLAPATISLRMLCAAAVSYSDNTAGNRILTYLGGPDAVTQFMRGIGDPVTRLDRTEPTLNEATPGDARDTSSPQKMAAGLQKILTAPPLTPANRAVLAQWMRDDKVGDALLRAALPKGWAIADKTGAGGYGSRAIIAAVYPPERPPFYVAIFITQTEASMKMANEAIPAIGKQLFAGQP"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms."}, "41641": {"category_aro_name": "HERA beta-lactamase", "category_aro_cvterm_id": "41641", "category_aro_accession": "3004447", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "A class A beta-lactamase family shown to hydrolyze penicillin but without cephalosporinase activity."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}}, "ARO_name": "HERA-8", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "42952", "model_name": "HERA-8", "model_type_id": "40292"}, "3617": {"model_id": "3617", "ARO_accession": "3003142", "model_param": {"blastp_bit_score": {"param_value": "600", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with 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. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "From the Lahey list of beta-lactamases. Not yet released.", "model_sequences": {"sequence": {"5815": {"dna_sequence": {"partial": "0", "sequence": "ATGTCAATTAATGCAAAGAAAAGTAAAGCAGCTGTCTTTTTAAGCTATTTTTTAATCCCTATATCATTTTATTCACAGGCTGATACAAATGCCATGGATGAGATTAAGAAACTGGAAACAGGTTTTGGTGGCAGGGTTGGCGTCTACGCTTTAGACACTGGCTCTGGTAAATCATTTTCATACAGAGCGAATGAACGATTTCCTCTTTGTAGTTCTTTTAAAGGTTTTTTAGCCGCTGCTGTATTAAAGGGCTCGCAGGATAATCAACTGAATATTAATGAGATTGTAAATTATAATAAAAGAAGTTTAGAACCCCACTCCCCTATTACGCAAAAATATAAAGAAAACGGAATGTCTCTAGGTGATATGGCTGCTGCCGCTTTACAATATAGCGACAATGGTGCTGCTAATATTATTCTTGAGCGTTATATCGGTGGTCCTGAAGGTATGACTAATTTCATGCGGTCTATTGGAGATGAAGACTTTAGACTCGATCGTTGGGAGTTAGATCTAAATACAGCTATTCCTGGCGATGAACGTGACACTTCAACACCCGCAGCTGTAGGTAAAAGTTTAAAAAACCTTGCTCTGGGCAATATACTTAACGATCATGAAAAGGAAACATATCAGACATGGTTAAAGGGTAATACAACCGGCGCAGCGCGTATTCGTGCTAGCGTACCAAGCGACTGGGTCGTTGGCGATAAAACCGGTACTTGTGGAGCATACGGTACGGCAAATGATTATGCGGTTGTCTGGCCAAAAAACAGGGCTCCTCTTATCATTTCTGTGTACACTACAAAAAGTGAAAAAGAAGCAAAGCATGACGAGAAGGTAATCGAAGAAGCTTCAAGAATTGCAATTACACACCTTAAGTAA", "fmax": "879", "accession": "KP081315.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Enterobacter cloacae", "NCBI_taxonomy_id": "550", "NCBI_taxonomy_cvterm_id": "36884"}, "protein_sequence": {"accession": "AIY69088.1", "sequence": "MSINAKKSKAAVFLSYFLIPISFYSQADTNAMDEIKKLETGFGGRVGVYALDTGSGKSFSYRANERFPLCSSFKGFLAAAVLKGSQDNQLNINEIVNYNKRSLEPHSPITQKYKENGMSLGDMAAAALQYSDNGAANIILERYIGGPEGMTNFMRSIGDEDFRLDRWELDLNTAIPGDERDTSTPAAVGKSLKNLALGNILNDHEKETYQTWLKGNTTGAARIRASVPSDWVVGDKTGTCGAYGTANDYAVVWPKNRAPLIISVYTTKSEKEAKHDEKVIEEASRIAITHLK"}}}}, "ARO_category": {"35939": {"category_aro_name": "carbapenem", "category_aro_cvterm_id": "35939", "category_aro_accession": "0000020", "category_aro_class_name": "Drug Class", "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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "36027": {"category_aro_name": "IMI beta-lactamase", "category_aro_cvterm_id": "36027", "category_aro_accession": "3000018", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "IMI beta-lactamases are a group of TEM-1-like beta-lactamase that are known to hydrolyze imipenem. IMI beta-lactamases are inhibited by clavulanic acid and tazobactam."}}, "ARO_name": "IMI-8", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "39719", "model_name": "IMI-8", "model_type_id": "40292"}, "3618": {"model_id": "3618", "ARO_accession": "3003657", "model_param": {"blastp_bit_score": {"param_value": "500", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with 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. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "From Lahey's list of beta-lactamases, no additional information available", "model_sequences": {"sequence": {"5816": {"dna_sequence": {"partial": "0", "sequence": "ATGAAAAAATTATTTGTTTTATGTGTATTCTTCCTTTGCAACATTGCTGCTGCAGATGATTCTTTGCCTGATTTAAAAATTGAGAAGCTTGAAAAAGGCGTTTATGTTCATACTTCGTTTGAAGAAGTTAAAGGTTGGGGTGTATTCACAAAACACGGTTTAGTGGTTCTTGTAAAGAATGATGCTTATCTGATAGATACTCCAATTACCGCTAAAGATACTGAAAAATTAGTTAATTGGTTTATTGAGCACGGCTATAGAATCAAAGGCAGTATTTCCACACATTTCCATGGCGACAGTACGGCTGGAATAGAGTGGCTTAATTCTCAATCTATCTCCACGTATGCCTCTGAATTAACAAATGAACTTCTAAAAAAAGACAATAAGGTGCAAGCTACAAATTCTTTTAGTGGAGTTAGTTATTCACTTATCAAAAACAAAATTGAAGTTTTCTATCCAGGTCCAGGACACACTCAAGATAACGTAGTGGTTTGGTTACCTGAAAAGAAAATTTTATTCGGTGGTTGCTTTGTTAAACCGGACGGTCTTGGAAATTTAGGGGATGCAAATTTAGAAGCTTGGCCAAAGTCCGCTAAAATATTAATGTCTAAATATGGTAAAGCAAAACTGGTTGTTTCAAGTCATAGTGAAATTGGAAACGCATCACTCTTGCAGCGCACATGGGAGCAGGCTGTTAAAGGGTTAAATGAAAGTAAAAAACCGTTACAGCCAAGTAGCTAA", "fmax": "741", "accession": "KP681694", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Pseudomonas aeruginosa", "NCBI_taxonomy_id": "287", "NCBI_taxonomy_cvterm_id": "36752"}, "protein_sequence": {"accession": "AKO63210.1", "sequence": "MKKLFVLCVFFLCNIAAADDSLPDLKIEKLEKGVYVHTSFEEVKGWGVFTKHGLVVLVKNDAYLIDTPITAKDTEKLVNWFIEHGYRIKGSISTHFHGDSTAGIEWLNSQSISTYASELTNELLKKDNKVQATNSFSGVSYSLIKNKIEVFYPGPGHTQDNVVVWLPEKKILFGGCFVKPDGLGNLGDANLEAWPKSAKILMSKYGKAKLVVSSHSEIGNASLLQRTWEQAVKGLNESKKPLQPSS"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "40360": {"category_aro_name": "penem", "category_aro_cvterm_id": "40360", "category_aro_accession": "3003706", "category_aro_class_name": "Drug Class", "category_aro_description": "Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur."}, "35939": {"category_aro_name": "carbapenem", "category_aro_cvterm_id": "35939", "category_aro_accession": "0000020", "category_aro_class_name": "Drug Class", "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."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36029": {"category_aro_name": "IMP beta-lactamase", "category_aro_cvterm_id": "36029", "category_aro_accession": "3000020", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors."}, "35962": {"category_aro_name": "cephamycin", "category_aro_cvterm_id": "35962", "category_aro_accession": "0000044", "category_aro_class_name": "Drug Class", "category_aro_description": "Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins 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. The 7-alpha-methoxy group increases resistance to beta-lactamases."}}, "ARO_name": "IMP-49", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "40267", "model_name": "IMP-49", "model_type_id": "40292"}, "3620": {"model_id": "3620", "ARO_accession": "3004825", "model_param": {"blastp_bit_score": {"param_value": "585", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with 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. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "LAP-1 is an Ambler Class A beta-lactamase gene conferring resistance to quinolones.", "model_sequences": {"sequence": {"5818": {"dna_sequence": {"partial": "0", "sequence": "ATGAAAAAGATCCGCCTTATTATAATCTCTTTACTGGCTGGAATGTGTACTCCAGCATTATCTACACCAGTCAATGTTACTGATACAATACAAAGCACAGAAGACCATATCAAAGGTCGGGTTGGTTTTACTGAAATAGACTTTTTATCCGGGAAGGTTCTGAGTAGTCATCGCCGTGAAGAACGTTTTCCTATGATGAGCACATTCAAAGTTTTGTTATGTGGAGCAATATTAGTACGTGTTGATAAAGGGCTTGAACAACTTGAACGCCGAATTACCTATAATAAGCATGACCTGGACGACTATTCTCCACTAACCAGTCAGCACATTGCAGATGGAATGACGGTTTCTGAGTTATGCAATGCTGCCATTACCACCAGTGATAACACTGCTGCAAATTTATTGCTATCAACTATTGGCGGGCCGGAGGGATTAACTCATTTTCTGCGTAGCACTGGTGATAGTTATACAAGGCTTGATCGACACGAACCCAGCCTTAATGAGGCGAAGCCTGGCGATGAGCGTGATACCACCACTCCGGCAGCGATGGCTCAAACGCTACAAAAATTGTTAAACGGAAGTGTACTTACAGAAAAATCTCGAAAAAAATTAATAAGCTGGATGCAGGAAGATAAAGTCGGCGGGCCTCTGTTCCGCTCTGTACTGCCAGCTGGCTGGATGATAGCGGATAAAACAGGAGCAGGTGATCACGGATCTCGGGGCATCGTTGCACTGTTGGGCCCCGGAGGCAAGCCATCTCGTATAGTAGTCCTGTATATTACAAATACTCATTCATCTATGAATGAACTCAACGAGCATATTGCAGGGATCGGAGATTCAGTAATTAAGAACTGGTAA", "fmax": "858", "accession": "EF026092.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Enterobacter cloacae", "NCBI_taxonomy_id": "550", "NCBI_taxonomy_cvterm_id": "36884"}, "protein_sequence": {"accession": "ABK58097.1", "sequence": "MKKIRLIIISLLAGMCTPALSTPVNVTDTIQSTEDHIKGRVGFTEIDFLSGKVLSSHRREERFPMMSTFKVLLCGAILVRVDKGLEQLERRITYNKHDLDDYSPLTSQHIADGMTVSELCNAAITTSDNTAANLLLSTIGGPEGLTHFLRSTGDSYTRLDRHEPSLNEAKPGDERDTTTPAAMAQTLQKLLNGSVLTEKSRKKLISWMQEDKVGGPLFRSVLPAGWMIADKTGAGDHGSRGIVALLGPGGKPSRIVVLYITNTHSSMNELNEHIAGIGDSVIKNW"}}}}, "ARO_category": {"36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "42954": {"category_aro_name": "LAP beta-lactamase", "category_aro_cvterm_id": "42954", "category_aro_accession": "3004824", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "LAP is a Ambler Class A beta-lactamase gene family that confers resistance to quinolones."}, "36189": {"category_aro_name": "tetracycline antibiotic", "category_aro_cvterm_id": "36189", "category_aro_accession": "3000050", "category_aro_class_name": "Drug Class", "category_aro_description": "These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes."}, "35920": {"category_aro_name": "fluoroquinolone antibiotic", "category_aro_cvterm_id": "35920", "category_aro_accession": "0000001", "category_aro_class_name": "Drug Class", "category_aro_description": "The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death."}, "35935": {"category_aro_name": "aminoglycoside antibiotic", "category_aro_cvterm_id": "35935", "category_aro_accession": "0000016", "category_aro_class_name": "Drug Class", "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."}, "36296": {"category_aro_name": "rifamycin antibiotic", "category_aro_cvterm_id": "36296", "category_aro_accession": "3000157", "category_aro_class_name": "Drug Class", "category_aro_description": "Rifamycin antibiotics are a group of broad-spectrum ansamycin antibiotics that inhibit bacterial RNA polymerase by binding to a highly conserved region, blocking the oligonucleotide exit tunnel, and preventing the extension of nascent mRNAs."}}, "ARO_name": "LAP-1", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "42955", "model_name": "LAP-1", "model_type_id": "40292"}, "3623": {"model_id": "3623", "ARO_accession": "3002479", "model_param": {"blastp_bit_score": {"param_value": "574", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with 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. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "LEN-25 is a beta-lactamase. From the Pasteur Institute list of LEN beta-lactamases.", "model_sequences": {"sequence": {"5821": {"dna_sequence": {"partial": "0", "sequence": "ATGCGTTATGTTCGCCTGTGTGTTATCTCCCTGTTAGCCACCCTGCCACTGGCGGTAGACGCCGGTCCACAGCCGCTTGAGCAGATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTGGGGATGGTGGAAATGGATCTGGCCAGCGGCCGCACGCTGGCCGCCTGGCGCGCCGATGAACGCTTTCCCATGGTGAGCACCTTTAAAGTGCTGCTGTGCGGCGCGGTGCTGGCGCGGGTGGATGCCGGGCTCGAACAACTGGATCGGCGGATCCACTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTGTCGACGGGATGGCGATCGGCGAACTCTGCGCCGCCGCCATCACCCTGAGCGATAACAGCGCTGGCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCGGGATTAACTGCCTTTCTGCGCCAGATCGGTGACAACGTCACCCGTCTTGACCGCTGGGAAACGGCACTGAATGAGGCGCTTCCCGGCGACGCGCGCGACACCACCACCCCGGCCAGCATGGCCGCCACGCTGCGCAAACTACTGACCGCGCAGCATCTGAGCGCCCGTTCGCAACAGCAACTCCTGCAGTGGATGGTGGACGATCGGGTTGCCGGCCCGCTGATCCGCGCCGTGCTGCCGCCGGGCTGGTTTATCGCCGACAAAACTGGGGCTGGCGAACGGGGTGCGCGCGGCATTGTCGCCCTGCTCGGCCCGGACGGCAAACCGGAGCGCATTGTGGTGCTCTATCTGCGGGATACCCCGGCGAGTATGGCCGAGCGTAATCAACATATCGCCGGGATCGGCGCAGCGCTGATCGAGCACTGGCAACGCTAA", "fmax": "861", "accession": "HQ709169.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Klebsiella pneumoniae", "NCBI_taxonomy_id": "573", "NCBI_taxonomy_cvterm_id": "35915"}, "protein_sequence": {"accession": "ADW77562.1", "sequence": "MRYVRLCVISLLATLPLAVDAGPQPLEQIKQSESQLSGRVGMVEMDLASGRTLAAWRADERFPMVSTFKVLLCGAVLARVDAGLEQLDRRIHYRQQDLVDYSPVSEKHLVDGMAIGELCAAAITLSDNSAGNLLLATVGGPAGLTAFLRQIGDNVTRLDRWETALNEALPGDARDTTTPASMAATLRKLLTAQHLSARSQQQLLQWMVDDRVAGPLIRAVLPPGWFIADKTGAGERGARGIVALLGPDGKPERIVVLYLRDTPASMAERNQHIAGIGAALIEHWQR"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms."}, "36236": {"category_aro_name": "LEN beta-lactamase", "category_aro_cvterm_id": "36236", "category_aro_accession": "3000097", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "LEN beta-lactamases are chromosomal class A beta-lactamases that confer resistance to ampicillin, amoxicillin, carbenicillin, and ticarcillin but not to extended-spectrum beta-lactams."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "40360": {"category_aro_name": "penem", "category_aro_cvterm_id": "40360", "category_aro_accession": "3003706", "category_aro_class_name": "Drug Class", "category_aro_description": "Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur."}}, "ARO_name": "LEN-25", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "38879", "model_name": "LEN-25", "model_type_id": "40292"}, "3622": {"model_id": "3622", "ARO_accession": "3002473", "model_param": {"blastp_bit_score": {"param_value": "576", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with 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. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "LEN-17 is a beta-lactamase found in Escherichia coli", "model_sequences": {"sequence": {"5820": {"dna_sequence": {"partial": "0", "sequence": "ATGCGTTATGTTCGCCTGTGTGTTATCTCCCTGTTAGCCACCCTGCCACTGGCGGTAGACGCCGGTCCACAGCCGCTTGAGCAGATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTGGGGATGGTGGAAATGGATCTGGCCAGCGGCCGCACGCTGGCCGCCTGGCGCGCCGATGAACGCTTTCCCATGGTGAGCACCTTTAAAGTGCTGCTGTGCGGCGCGGTGCTGGCGCGGGTGGATGCAGGGGTCGAACAACTGGATCGGCGGATCCACTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTACCGACGGGATGACGGTCGGCGAACTCTGCGCCGCCGCCATCACCCTGAGCGATAACAGTGCTGGCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCGGGATTAACTGCCTTTCTGCGCCAGATCGGTGACAACGTCACCCGTCTTGACCGCTGGGAAACGGCACTGAATGAGGCGCTTCCCGGCGACGCACGCGACACCACCACCCCGGCCAGCATGGCCGCCACGCTGCGCAAACTACTGACCGCGCAGCATCTGAGCGCCCGTTCGCAACAGCAACTCCTGCAGTGGATGGTGGACGATCGGGTTGCCGGCCCGCTGATCCGCGCCGTGCTGCCGCCGGGCTGGTTTATCGCCGACAAGACCGGGGCTGGCGAACGGGGTGCGCGCGGCATTGTCGCCCTGCTCGGCCCGGACGGCAAACCGGAGCGCATTGTGGTGATCTATCTGCGGGATACCCCGGCGAGCATGGCCGAGCGTAATCAACATATCGCCGGGATCGGCGCAGCGCTGATCGAGCACTGGCAACGCTAA", "fmax": "861", "accession": "DQ149134.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Klebsiella pneumoniae", "NCBI_taxonomy_id": "573", "NCBI_taxonomy_cvterm_id": "35915"}, "protein_sequence": {"accession": "AAZ79401.1", "sequence": "MRYVRLCVISLLATLPLAVDAGPQPLEQIKQSESQLSGRVGMVEMDLASGRTLAAWRADERFPMVSTFKVLLCGAVLARVDAGVEQLDRRIHYRQQDLVDYSPVSEKHLTDGMTVGELCAAAITLSDNSAGNLLLATVGGPAGLTAFLRQIGDNVTRLDRWETALNEALPGDARDTTTPASMAATLRKLLTAQHLSARSQQQLLQWMVDDRVAGPLIRAVLPPGWFIADKTGAGERGARGIVALLGPDGKPERIVVIYLRDTPASMAERNQHIAGIGAALIEHWQR"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms."}, "36236": {"category_aro_name": "LEN beta-lactamase", "category_aro_cvterm_id": "36236", "category_aro_accession": "3000097", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "LEN beta-lactamases are chromosomal class A beta-lactamases that confer resistance to ampicillin, amoxicillin, carbenicillin, and ticarcillin but not to extended-spectrum beta-lactams."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "40360": {"category_aro_name": "penem", "category_aro_cvterm_id": "40360", "category_aro_accession": "3003706", "category_aro_class_name": "Drug Class", "category_aro_description": "Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur."}}, "ARO_name": "LEN-17", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "38873", "model_name": "LEN-17", "model_type_id": "40292"}, "3625": {"model_id": "3625", "ARO_accession": "3004828", "model_param": {"blastp_bit_score": {"param_value": "576", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with 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. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "LEN-36 is a class A beta-lactamase gene found in Klebsiella variicola.", "model_sequences": {"sequence": {"5823": {"dna_sequence": {"partial": "0", "sequence": "ATGCGTTATGTTCGCCTGTGTGTTATCTCCCTGTTAGCCACCCTGCCACTGGCGGTAGACGCCGGTCCACAGCCGCTTGAGCAGATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTGGGGATGGTGGAAATGGATCTGGCCAGCGGCCACACGCTGGCCGCCTGGCGCGCCGATGAACGCTTTCCCATGGTGAGCACCTTTAAAGTGCTGCTGTGCGGCGCGGTGCTGGCGCGGGTGGATGCAGGGGTCGAACAACTGGATCGGCGGATCCACTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTACCGACGGGATGACGGTCGGCGAACTCTGCGCCGCCGCCATCACCCTGAGCGATAACAGTGCTGGCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCGGGATTAACTGCCTTTCTGCGCCAGATCGGTGACAACGTCACCCGTCTTGACCGCTGGGAAACGGCACTGAATGAGGCGCTTCCCGGCGACGCACGCGACACCACCACCCCGGCCAGCATGGCCGCCACGCTGCGCAAACTACTGACCGCGCAGCATCTGAGCGCCCGTTCGCAACAGCAACTCCTGCAGTGGATGGTGGACGATCGGGTTGCCGGCCCGCTGATCCGCGCCGTGCTGCCGCCGGGCTGGTTTATCGCCGACAAGACCGGGGCTGGCGAACGGGGTGCGCGCGGCATTGTCGCCCTGCTCGGCCCGGACGGCAAACCGGAGCGCATTGTGGTGATCTATCTGCGGGATACCCCGGCGAGCATGGCCGAGCGTAATCAACATATCGCCGGGATCGGCGCAGCGCTGATCGAGCACTGGCAACGCTAA", "fmax": "861", "accession": "KR738738.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Klebsiella variicola", "NCBI_taxonomy_id": "244366", "NCBI_taxonomy_cvterm_id": "42612"}, "protein_sequence": {"accession": "ALK01319.1", "sequence": "MRYVRLCVISLLATLPLAVDAGPQPLEQIKQSESQLSGRVGMVEMDLASGHTLAAWRADERFPMVSTFKVLLCGAVLARVDAGVEQLDRRIHYRQQDLVDYSPVSEKHLTDGMTVGELCAAAITLSDNSAGNLLLATVGGPAGLTAFLRQIGDNVTRLDRWETALNEALPGDARDTTTPASMAATLRKLLTAQHLSARSQQQLLQWMVDDRVAGPLIRAVLPPGWFIADKTGAGERGARGIVALLGPDGKPERIVVIYLRDTPASMAERNQHIAGIGAALIEHWQR"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms."}, "36236": {"category_aro_name": "LEN beta-lactamase", "category_aro_cvterm_id": "36236", "category_aro_accession": "3000097", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "LEN beta-lactamases are chromosomal class A beta-lactamases that confer resistance to ampicillin, amoxicillin, carbenicillin, and ticarcillin but not to extended-spectrum beta-lactams."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "40360": {"category_aro_name": "penem", "category_aro_cvterm_id": "40360", "category_aro_accession": "3003706", "category_aro_class_name": "Drug Class", "category_aro_description": "Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur."}}, "ARO_name": "LEN-36", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "42958", "model_name": "LEN-36", "model_type_id": "40292"}, "3624": {"model_id": "3624", "ARO_accession": "3004827", "model_param": {"blastp_bit_score": {"param_value": "575", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with 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. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "LEN-35 is a Class A beta-lactamase gene found in Klebsiella variicola.", "model_sequences": {"sequence": {"5822": {"dna_sequence": {"partial": "0", "sequence": "ATGCGTTATATTCGCCTGTGTGTTATCTCCCTGTTAGCCACCCTGCCACTGGCGGTATACGCCGGTCCACAGCCGCTTGAGCAGATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTGGGGATGGTGGAAATGGATCTGGCCAGCGGCCGCACGCTGGCGGCCTGGCGCGCCGATGAACGCTTTCCCATGGTGAGCACCTTTAAAGTGCTGCTGTGCGGCGCGGTGCTGGCGCGGGTGGATGCCGGGCTCGAACAACTGGATCGGCGGATCCACTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTACCGACGGGATGACGGTCGGCGAACTCTGCGCCGCCGCCATCACCCTGAGCGATAACAGCGCTGGCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCGGGATTAACTGCCTTTCTGCGCCAGATCGGTGACAACGTCACCCGTCTTGACCGCTGGGAAACGGCACTGAATGAGGCGCTTCCCGGCGACGCGCGCGACACCACCACCCCGGCCAGCATGGCTGCCACGCTGCGCAAACTACTGACCGCGCAGCATCTGAGCGCCCGTTCGCAACAGCAACTCCTGCAGTGGATGGTGGACGATCGGGTTGCCGGCCCGCTGATCCGCGCCGTGCTGCCGCCGGGCTGGTTTATCGCCGACAAAACCGGGGCTGGCGAACGGGGTGCGCGCGGCATTGTCGCCCTGCTCGGCCCGGACGGCAAACCGGAGCGCATTGTGGTGATCTATCTGCGGGATACCCCGGCGAGTATGGCCGAGCGTAATCAACATATCGCCGGGATCGGCGCAGCGCTGATCGAGCACTGGCACGACTAA", "fmax": "861", "accession": "KR738737.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Klebsiella variicola", "NCBI_taxonomy_id": "244366", "NCBI_taxonomy_cvterm_id": "42612"}, "protein_sequence": {"accession": "ALK01318.1", "sequence": "MRYIRLCVISLLATLPLAVYAGPQPLEQIKQSESQLSGRVGMVEMDLASGRTLAAWRADERFPMVSTFKVLLCGAVLARVDAGLEQLDRRIHYRQQDLVDYSPVSEKHLTDGMTVGELCAAAITLSDNSAGNLLLATVGGPAGLTAFLRQIGDNVTRLDRWETALNEALPGDARDTTTPASMAATLRKLLTAQHLSARSQQQLLQWMVDDRVAGPLIRAVLPPGWFIADKTGAGERGARGIVALLGPDGKPERIVVIYLRDTPASMAERNQHIAGIGAALIEHWHD"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms."}, "36236": {"category_aro_name": "LEN beta-lactamase", "category_aro_cvterm_id": "36236", "category_aro_accession": "3000097", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "LEN beta-lactamases are chromosomal class A beta-lactamases that confer resistance to ampicillin, amoxicillin, carbenicillin, and ticarcillin but not to extended-spectrum beta-lactams."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "40360": {"category_aro_name": "penem", "category_aro_cvterm_id": "40360", "category_aro_accession": "3003706", "category_aro_class_name": "Drug Class", "category_aro_description": "Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur."}}, "ARO_name": "LEN-35", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "42957", "model_name": "LEN-35", "model_type_id": "40292"}, "3627": {"model_id": "3627", "ARO_accession": "3001063", "model_param": {"blastp_bit_score": {"param_value": "550", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with 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. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "SHV-4 is an extended-spectrum beta-lactamase that has been found in clinical isolates.", "model_sequences": {"sequence": {"5835": {"dna_sequence": {"partial": "0", "sequence": "ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTACTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACTGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTAGCAAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATCGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA", "fmax": "36968", "accession": "LT985229.1", "fmin": "36107", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Escherichia coli", "NCBI_taxonomy_id": "562", "NCBI_taxonomy_cvterm_id": "35914"}, "protein_sequence": {"accession": "SPD96731.1", "sequence": "MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQLQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGASKRGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"}}}}, "ARO_category": {"35939": {"category_aro_name": "carbapenem", "category_aro_cvterm_id": "35939", "category_aro_accession": "0000020", "category_aro_class_name": "Drug Class", "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."}, "36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "36024": {"category_aro_name": "SHV beta-lactamase", "category_aro_cvterm_id": "36024", "category_aro_accession": "3000015", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known."}}, "ARO_name": "SHV-4", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "37443", "model_name": "SHV-4", "model_type_id": "40292"}, "3626": {"model_id": "3626", "ARO_accession": "3004829", "model_param": {"blastp_bit_score": {"param_value": "576", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with 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. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "LEN-37 is a Class A beta-lactamase gene found in Klebsiella variicola.", "model_sequences": {"sequence": {"5824": {"dna_sequence": {"partial": "0", "sequence": "ATGCGTTATGTTCGCCTTTGTGTTATCTCCCTGTTAGCCACCCTGCCACTGGCGGTAGACGCCGGTCCACAGCCGCTTGAGCAGATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTGGGGATGGTGGAAATGGATCTGGCCAGCGGCCGCACACTGGCCGCCTGGCGCGCCGATGAACGCTTTCCCATGGTGAGCACCTTTAAAGTGCTGCTGTGCGGCGCGGTGCTGGCGCGGGTGGATGCAGGGGTCGAACAACTGGATCGGCGGATCCACTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTGTCGACGGGATGACGATCGGCGAACTCTGCGCCGCCGCCATCACCCTGAGCGATAACAGCGCTGGCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCGGGATTAACTGCCTTTCTACGCCAGATCGGTGACAACGTCACCCGTCTTGACCGCTGGGAAACGGCACTGAATGAGGCGCTTCCCGGCGACGCGCGCGACACCACCACCCCGGCCAGCATGTCCGCCACGCTGCGCAAACTACTGACCGCGCAGCATCTGAGCGCCCGTTCGCAACAGCAACTCCTGCAGTGGATGGTGGACGATCGGGTTGCCGGCCCGCTGATCCGCGCCGTGCTGCCGCCGGGCTGGTTTATCGCCGACAAAACCGGGGCTGGCGAACGGGGTGCGCGCGGCATTGTCGCCCTGCTCGGCCCGGACGGCAAACCGGAGCGCATTGTGGTGATCTATCTGCGGGATACCCCGGCGAGTATGGCCGAGCGTAATCAACATATCGCCGGGATCGGCGCAGCGCTGATCGAGCACTGGCAACGCTAA", "fmax": "861", "accession": "KR738739.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Klebsiella variicola", "NCBI_taxonomy_id": "244366", "NCBI_taxonomy_cvterm_id": "42612"}, "protein_sequence": {"accession": "ALK01320.1", "sequence": "MRYVRLCVISLLATLPLAVDAGPQPLEQIKQSESQLSGRVGMVEMDLASGRTLAAWRADERFPMVSTFKVLLCGAVLARVDAGVEQLDRRIHYRQQDLVDYSPVSEKHLVDGMTIGELCAAAITLSDNSAGNLLLATVGGPAGLTAFLRQIGDNVTRLDRWETALNEALPGDARDTTTPASMSATLRKLLTAQHLSARSQQQLLQWMVDDRVAGPLIRAVLPPGWFIADKTGAGERGARGIVALLGPDGKPERIVVIYLRDTPASMAERNQHIAGIGAALIEHWQR"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms."}, "36236": {"category_aro_name": "LEN beta-lactamase", "category_aro_cvterm_id": "36236", "category_aro_accession": "3000097", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "LEN beta-lactamases are chromosomal class A beta-lactamases that confer resistance to ampicillin, amoxicillin, carbenicillin, and ticarcillin but not to extended-spectrum beta-lactams."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "40360": {"category_aro_name": "penem", "category_aro_cvterm_id": "40360", "category_aro_accession": "3003706", "category_aro_class_name": "Drug Class", "category_aro_description": "Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur."}}, "ARO_name": "LEN-37", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "42959", "model_name": "LEN-37", "model_type_id": "40292"}, "3621": {"model_id": "3621", "ARO_accession": "3004826", "model_param": {"blastp_bit_score": {"param_value": "585", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with 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. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "LAP-2 is an Ambler Class A beta-lactamase gene conferring resistance to quinolones.", "model_sequences": {"sequence": {"5819": {"dna_sequence": {"partial": "0", "sequence": "ATGAAAAAGATCCGCCTTATTATAATCTCTTTACTGGCTGGAATGTGTACTCCAGCATTATCTACACCAGTCAATGTTACTGATACAATACAAAGCACAGAAGACCATATCAAAGGTCGGGTTGGTTTTACTGAAATAGACTTTTTATCCGGGAAGGTTCTGAGTAGTCATCGCCGTGAAGAACGTTTTCCTATGATGAGCACATTCAAAGTTTTGTTATGTGGAGCAATATTAGTACGTGTTGATAAAGGGCTTGAACAACTTGAACGCCGAATTACCTATAATAAGCATGACCTGGACGACTATTCTCCACTAACCAGTCAGCACATTGCAGATGGAATGACGGTTTCTGAGTTATGCAATGCTGCCATTACCACCAGTGATAACACTGCTGCAAATTTATTGCTATCAACTATTGGCGGGCCGGAGGGATTAACTCATTTTCTGCGTAGCACTGGTGATAGTTATACAAGGCTTGATCGACACGAACCCAGCCTTAATGAGGCGAAGCCTGGCGATGAGCGTGATACCACCACTCCGGCAGCGATGGCTCAAACGCTACAAAAATTGTTAAACGAAAGTGTACTTACAGAAAAATCTCGAAAAAAATTAATAAGCTGGATGCAGGAAGATAAAGTCGGCGGGCCTCTGTTCCGCTCTGTACTGCCAGCTGGCTGGATGATAGCGGATAAAACAGGAGCAGGTGATCACGGATCTCGGGGCATCGTTGCACTGTTGGGCCCCGGAGGCAAGCCATCTCGTATAGTAGTCCTGTATATTACAAATACTCATTCATCTATGAATGAACTCAACGAGCATATTGCAGGGATCGGAGATTCAGTAATTAAGAACTGGTAA", "fmax": "858", "accession": "EU159120.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Enterobacter cloacae", "NCBI_taxonomy_id": "550", "NCBI_taxonomy_cvterm_id": "36884"}, "protein_sequence": {"accession": "ABV89601.1", "sequence": "MKKIRLIIISLLAGMCTPALSTPVNVTDTIQSTEDHIKGRVGFTEIDFLSGKVLSSHRREERFPMMSTFKVLLCGAILVRVDKGLEQLERRITYNKHDLDDYSPLTSQHIADGMTVSELCNAAITTSDNTAANLLLSTIGGPEGLTHFLRSTGDSYTRLDRHEPSLNEAKPGDERDTTTPAAMAQTLQKLLNESVLTEKSRKKLISWMQEDKVGGPLFRSVLPAGWMIADKTGAGDHGSRGIVALLGPGGKPSRIVVLYITNTHSSMNELNEHIAGIGDSVIKNW"}}}}, "ARO_category": {"36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "42954": {"category_aro_name": "LAP beta-lactamase", "category_aro_cvterm_id": "42954", "category_aro_accession": "3004824", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "LAP is a Ambler Class A beta-lactamase gene family that confers resistance to quinolones."}, "36189": {"category_aro_name": "tetracycline antibiotic", "category_aro_cvterm_id": "36189", "category_aro_accession": "3000050", "category_aro_class_name": "Drug Class", "category_aro_description": "These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes."}, "35920": {"category_aro_name": "fluoroquinolone antibiotic", "category_aro_cvterm_id": "35920", "category_aro_accession": "0000001", "category_aro_class_name": "Drug Class", "category_aro_description": "The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death."}, "35935": {"category_aro_name": "aminoglycoside antibiotic", "category_aro_cvterm_id": "35935", "category_aro_accession": "0000016", "category_aro_class_name": "Drug Class", "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."}, "36296": {"category_aro_name": "rifamycin antibiotic", "category_aro_cvterm_id": "36296", "category_aro_accession": "3000157", "category_aro_class_name": "Drug Class", "category_aro_description": "Rifamycin antibiotics are a group of broad-spectrum ansamycin antibiotics that inhibit bacterial RNA polymerase by binding to a highly conserved region, blocking the oligonucleotide exit tunnel, and preventing the extension of nascent mRNAs."}}, "ARO_name": "LAP-2", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "42956", "model_name": "LAP-2", "model_type_id": "40292"}, "3619": {"model_id": "3619", "ARO_accession": "3004823", "model_param": {"blastp_bit_score": {"param_value": "495", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with 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. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "IMP-52 is a class B metallo-beta-lactamase found in Escherichia coli.", "model_sequences": {"sequence": {"5817": {"dna_sequence": {"partial": "0", "sequence": "ATGAGCAAGTTATCTGTATTCTTTATATTTTTGTTTTGCAGCATTGCTACCGCAGCAGAGTCTTTGCCAGATTTAAAAATTGAAAAGCTTGATGAAGGCGTTTATGTTCATACTTCGTTTGAAGAAGTTAACGGGTGGGGCGTTGTTCCTAAACATGGTTTGGTGGTTCTTGTAAATGCTGAGGCTTACATAATTGACACTCCATTTACGGCTAAAGATACTGAAAAGTTAGGCACTTGGTTTGTGGAGCGTGGCTATAAAATAAAAGGCAGCATTTCCTCTCATTTTCATAGCGACAGCACGGGCGGAATAGAGTGGCTTAATTCTCGATCTATCCCCACGTATGCATCTGAATTAACAAATGAACTGCTTAAAAAAGACGGTAAGGTTCAAGCCACAAATTCATTTAGCGGAGTTAACTATTGGCTAGTTAAAAATAAAATTGAAGTTTTTTATCCAGGCCCGGGACACACTCCAGATAACGTAGTGGTTTGGTTGCCTGAAAGGAAAATATTATTCGGTGGTTGTTTTATTAAACCGTACGGTTTAGGCAATTTGGGTGACGCAAATATAGAAGCTTGGCCAAAGTCCGCCAAATTATTAAAGTCCAAATATGGTAAGGCAAAACTGGTTGTTCCAAGTCACAGTGAAGTTGGAGACGCATCACTCTTGAAACTTACATTAGAGCAGGCGGTTAAAGGGTTAAACGAAAGTAAAAAACCATCAAAACCAAGCAACTAA", "fmax": "1306", "accession": "LC055762", "fmin": "565", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Escherichia coli", "NCBI_taxonomy_id": "562", "NCBI_taxonomy_cvterm_id": "35914"}, "protein_sequence": {"accession": "BAR80870.1", "sequence": "MSKLSVFFIFLFCSIATAAESLPDLKIEKLDEGVYVHTSFEEVNGWGVVPKHGLVVLVNAEAYIIDTPFTAKDTEKLGTWFVERGYKIKGSISSHFHSDSTGGIEWLNSRSIPTYASELTNELLKKDGKVQATNSFSGVNYWLVKNKIEVFYPGPGHTPDNVVVWLPERKILFGGCFIKPYGLGNLGDANIEAWPKSAKLLKSKYGKAKLVVPSHSEVGDASLLKLTLEQAVKGLNESKKPSKPSN"}}}}, "ARO_category": {"36017": {"category_aro_name": "penam", "category_aro_cvterm_id": "36017", "category_aro_accession": "3000008", "category_aro_class_name": "Drug Class", "category_aro_description": "Penams, often referred to as penicillins, are a group of antibiotics derived from Penicillium fungi. Penicillin antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms."}, "36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "40360": {"category_aro_name": "penem", "category_aro_cvterm_id": "40360", "category_aro_accession": "3003706", "category_aro_class_name": "Drug Class", "category_aro_description": "Penems are a class of unsaturated beta-lactam antibiotics with a broad spectrum of antibacterial activity and have a structure which renders them highly resistant to beta-lactamases. All penems are all synthetically made and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. They are structurally similar to carbapenems, however, where carbapenems have a carbon, penems have a sulfur."}, "35939": {"category_aro_name": "carbapenem", "category_aro_cvterm_id": "35939", "category_aro_accession": "0000020", "category_aro_class_name": "Drug Class", "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."}, "35951": {"category_aro_name": "cephalosporin", "category_aro_cvterm_id": "35951", "category_aro_accession": "0000032", "category_aro_class_name": "Drug Class", "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."}, "36029": {"category_aro_name": "IMP beta-lactamase", "category_aro_cvterm_id": "36029", "category_aro_accession": "3000020", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors."}, "35962": {"category_aro_name": "cephamycin", "category_aro_cvterm_id": "35962", "category_aro_accession": "0000044", "category_aro_class_name": "Drug Class", "category_aro_description": "Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins 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. The 7-alpha-methoxy group increases resistance to beta-lactamases."}}, "ARO_name": "IMP-52", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "42953", "model_name": "IMP-52", "model_type_id": "40292"}}}