Model Type : protein variant model
Model Definition : Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.
Bit-score Cut-off (blastP) : 3575
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discovered in clinical, agricultural, or environmental isolates discovered via laboratory selection experiments ReSeqTB https://platform.reseqtb.org Published Variants :
PMID in progress (TB): M127I V295M A437P P563H A1248T I1508L V1522A A1639V E1823A
ReSeqTB :
COPY
>gb|CCP45737.1|+|Mycobacterium tuberculosis ppsD mutations confer resistance to pyrazinamide [Mycobacterium tuberculosis H37Rv]
MTSLAERAAQLSPNARAALARELVRAGTTFPTDICEPVAVVGIGCRFPGNVTGPESFWQLLADGVDTIEQVPPDRWDADAFYDPDPSASGRMTTKWGGFVSDVDAFDADFFGITPREAVAMDPQHRMLLEVAWEALEHAGIPPDSLSGTRTGVMMGLSSWDYTIVNIERRADIDAYLSTGTPHCAAVGRIAYLLGLRGPAVAVDTACSSSLVAIHLACQSLRLRETDVALAGGVQLTLSPFTAIALSKWSALSPTGRCNSFDANADGFVRGEGCGVVVLKRLADAVRDQDRVLAVVRGSATNSDGRSNGMTAPNALAQRDVITSALKLADVTPDSVNYVETHGTGTVLGDPIEFESLAATYGLGKGQGESPCALGSVKTNIGHLEAAAGVAGFIKAVLAVQRGHIPRNLHFTRWNPAIDASATRLFVPTESAPWPAAAGPRRAAVSSFGLSGTNAHVVVEQAPDTAVAAAGGMPYVSALNVSGKTAARVASAAAVLADWMSGPGAAAPLADVAHTLNRHRARHAKFATVIARDRAEAIAGLRALAAGQPRVGVVDCDQHAGGPGRVFVYSGQGSQWASMGQQLLANEPAFAKAVAELDPIFVDQVGFSLQQTLIDGDEVVGIDRIQPVLVGMQLALTELWRSYGVIPDAVIGHSMGEVSAAVVAGALTPEQGLRVITTRSRLMARLSGQGAMALLELDADAAEALIAGYPQVTLAVHASPRQTVIAGPPEQVDTVIAAVATQNRLARRVEVDVASHHPIIDPILPELRSALADLTPQPPSIPIISTTYESAQPVADADYWSANLRNPVRFHQAVTAAGVDHNTFIEISPHPVLTHALTDTLDPDGSHTVMSTMNRELDQTLYFHAQLAAVGVAASEHTTGRLVDLPPTPWHHQRFWVTDRSAMSELAATHPLLGAHIEMPRNGDHVWQTDVGTEVCPWLADHKVFGQPIMPAAGFAEIALAAASEALGTAADAVAPNIVINQFEVEQMLPLDGHTPLTTQLIRGGDSQIRVEIYSRTRGGEFCRHATAKVEQSPRECAHAHPEAQGPATGTTVSPADFYALLRQTGQHHGPAFAALSRIVRLADGSAETEISIPDEAPRHPGYRLHPVVLDAALQSVGAAIPDGEIAGSAEASYLPVSFETIRVYRDIGRHVRCRAHLTNLDGGTGKMGRIVLINDAGHIAAEVDGIYLRRVERRAVPLPLEQKIFDAEWTESPIAAVPAPEPAAETTRGSWLVLADATVDAPGKAQAKSMADDFVQQWRSPMRRVHTADIHDESAVLAAFAETAGDPEHPPVGVVVFVGGASSRLDDELAAARDTVWSITTVVRAVVGTWHGRSPRLWLVTGGGLSVADDEPGTPAAASLKGLVRVLAFEHPDMRTTLVDLDITQDPLTALSAELRNAGSGSRHDDVIAWRGERRFVERLSRATIDVSKGHPVVRQGASYVVTGGLGGLGLVVARWLVDRGAGRVVLGGRSDPTDEQCNVLAELQTRAEIVVVRGDVASPGVAEKLIETARQSGGQLRGVVHAAAVIEDSLVFSMSRDNLERVWAPKATGALRMHEATADCELDWWLGFSSAASLLGSPGQAAYACASAWLDALVGWRRASGLPAAVINWGPWSEVGVAQALVGSVLDTISVAEGIEALDSLLAADRIRTGVARLRADRALVAFPEIRSISYFTQVVEELDSAGDLGDWGGPDALADLDPGEARRAVTERMCARIAAVMGYTDQSTVEPAVPLDKPLTELGLDSLMAVRIRNGARADFGVEPPVALILQGASLHDLTADLMRQLGLNDPDPALNNADTIRDRARQRAAARHGAAMRRRPKPEVQGG
>gb|CCP45737.1|+|Mycobacterium tuberculosis ppsD mutations confer resistance to pyrazinamide [Mycobacterium tuberculosis H37Rv] MTSLAERAAQLSPNARAALARELVRAGTTFPTDICEPVAVVGIGCRFPGNVTGPESFWQLM LLEVAWEALEHAGIPPDSLSGTRTGVMMGLSSWDYTIVNIERRADIDAYLSTGV VRGSAA AGPRRAAVSSFGLSGTNAHVVVEQAPDTAVAAAGGMPYVSALNP GRVFVYSGQGSQWASMGQQLLANEPAFAKAVAELDPIA KSMADDFVQQWRI ETARQSGGQLRGVV HAAAVIEDSLVFSMSRDNLERVWAPKATGALRMHEATAA LDSLLAADRIRTGVARLRADRALVAFPEIRSISYFTQVVEEE VQGG COPY
>gb|AL123456.3|+|3262248-3267731|Mycobacterium tuberculosis ppsD mutations confer resistance to pyrazinamide [Mycobacterium tuberculosis H37Rv]
>gb|AL123456.3|+|3262248-3267731|Mycobacterium tuberculosis ppsD mutations confer resistance to pyrazinamide [Mycobacterium tuberculosis H37Rv]
ATGACAAGTCTGGCGGAGCGCGCGGCGCAACTGTCGCCGAACGCGCGAGCGGCCCTGGCGCGCGAGCTCGTCCGTGCGGGTACGACCTTCCCGACCGACATCTGCGAGCCGGTGGCGGTGGTGGGCATCGGCTGTCGCTTTCCGGGGAATGTGACTGGGCCAGAGAGCTTTTGGCAGCTACTGGCCGACGGTGTGGACACAATCGAGCAGGTGCCGCCTGATCGGTGGGATGCGGACGCGTTCTACGATCCCGATCCTTCGGCGTCGGGTCGGATGACGACGAAATGGGGTGGTTTCGTTTCCGATGTCGACGCGTTCGACGCCGACTTTTTCGGAATCACTCCTCGGGAAGCCGTGGCGATGGACCCGCAGCATCGGATGCTGCTCGAGGTTGCCTGGGAAGCGTTGGAGCACGCGGGTATTCCGCCGGATTCCTTGAGCGGCACTCGAACCGGCGTGATGATGGGTCTGTCGTCGTGGGACTACACGATCGTCAATATCGAGCGCAGAGCCGACATCGACGCGTACCTGAGCACCGGAACCCCGCACTGTGCCGCGGTGGGGCGGATCGCGTATCTGTTGGGATTGCGTGGTCCGGCCGTCGCCGTAGATACCGCTTGTTCGTCGTCGCTGGTGGCAATTCACTTGGCGTGTCAGAGCCTTCGCCTGCGTGAAACCGACGTGGCATTGGCGGGCGGGGTGCAGCTCACCTTGTCACCGTTCACCGCCATCGCGCTGTCCAAGTGGTCGGCGCTGTCACCGACCGGCCGATGCAACAGCTTCGACGCCAACGCGGATGGATTCGTGCGCGGCGAGGGCTGCGGCGTGGTGGTGCTCAAGCGGTTGGCCGACGCGGTGCGCGACCAGGACCGGGTGCTTGCGGTGGTCCGCGGTTCGGCAACTAACTCCGATGGTCGGTCCAACGGCATGACCGCACCGAACGCGCTGGCGCAGCGTGACGTGATCACATCCGCCCTCAAGCTTGCGGATGTTACCCCTGACAGCGTGAACTATGTCGAAACACACGGCACCGGAACGGTGTTGGGGGACCCCATCGAGTTCGAGTCGCTGGCGGCCACTTATGGCCTGGGTAAAGGCCAGGGCGAGAGCCCGTGCGCATTGGGGTCGGTCAAGACCAACATCGGCCACCTGGAGGCGGCCGCCGGTGTGGCTGGATTCATCAAGGCGGTGCTGGCGGTGCAACGTGGGCACATTCCCCGCAACTTGCACTTCACCCGGTGGAACCCGGCCATCGACGCGTCGGCGACGCGGCTGTTCGTGCCGACCGAAAGCGCCCCGTGGCCGGCGGCTGCCGGTCCACGCAGGGCTGCGGTGTCATCGTTCGGCCTCAGCGGGACCAACGCGCACGTGGTGGTCGAGCAGGCACCCGACACCGCAGTAGCCGCAGCCGGCGGCATGCCGTATGTTTCGGCGCTGAACGTCTCCGGCAAGACGGCCGCGCGGGTGGCGTCGGCGGCGGCGGTGCTGGCCGACTGGATGTCGGGGCCGGGCGCGGCGGCACCACTGGCCGACGTGGCACACACGTTGAACCGGCACCGGGCCCGGCACGCCAAGTTCGCCACCGTCATCGCGCGTGACCGCGCCGAGGCGATCGCGGGGTTGCGAGCGCTGGCGGCCGGACAACCACGCGTTGGGGTGGTGGATTGCGACCAGCATGCCGGTGGGCCTGGCCGGGTTTTTGTGTATTCGGGTCAGGGCTCGCAGTGGGCGTCGATGGGCCAGCAGTTGCTGGCCAACGAACCGGCGTTCGCCAAGGCGGTAGCCGAGCTGGATCCGATATTCGTTGACCAGGTTGGCTTTTCGCTGCAGCAAACGCTTATCGACGGCGACGAGGTGGTGGGCATCGACCGCATCCAGCCGGTGCTGGTCGGGATGCAGTTGGCGCTGACCGAGTTATGGCGGTCCTATGGGGTGATTCCAGATGCCGTGATCGGGCACTCGATGGGTGAGGTGTCGGCGGCAGTGGTGGCCGGCGCGTTGACGCCCGAGCAGGGCTTGCGGGTCATCACCACCCGGTCGCGGTTGATGGCGCGGCTGTCGGGGCAGGGAGCGATGGCGCTGCTCGAGCTGGATGCCGACGCCGCCGAGGCGCTGATTGCCGGCTATCCGCAGGTGACGCTGGCGGTGCATGCGTCACCGCGCCAGACGGTGATCGCCGGGCCGCCCGAGCAGGTGGACACGGTGATCGCGGCGGTAGCGACGCAAAACCGGTTGGCGCGCCGCGTCGAAGTCGACGTGGCCTCCCATCACCCGATCATCGATCCCATACTGCCCGAGTTGCGAAGCGCGTTAGCGGATTTGACTCCGCAGCCGCCGAGCATCCCGATCATTTCCACTACGTACGAAAGCGCGCAGCCGGTGGCGGATGCCGACTATTGGTCGGCCAACCTGCGCAACCCGGTGCGATTCCACCAGGCCGTCACCGCCGCCGGTGTCGACCACAACACCTTCATCGAAATCAGCCCTCACCCCGTGCTCACGCACGCACTCACCGACACCCTGGATCCGGACGGCAGCCATACAGTCATGTCGACGATGAACCGCGAACTGGACCAGACGCTGTATTTCCACGCCCAACTCGCCGCGGTCGGTGTGGCTGCGTCCGAGCACACCACCGGTCGCCTTGTCGACCTGCCCCCCACACCGTGGCACCATCAGCGATTCTGGGTCACGGATCGTTCGGCGATGTCCGAGCTGGCCGCGACCCACCCGCTCCTGGGCGCGCACATCGAGATGCCGCGCAACGGAGACCATGTCTGGCAGACCGATGTCGGCACCGAGGTCTGTCCCTGGTTGGCAGACCACAAGGTGTTCGGTCAACCCATCATGCCGGCCGCGGGGTTCGCCGAGATCGCCTTGGCGGCGGCCAGCGAAGCCCTCGGCACAGCCGCCGACGCCGTCGCACCCAACATCGTGATCAACCAGTTCGAGGTGGAGCAGATGCTGCCCCTCGACGGCCACACGCCGCTAACGACGCAGTTAATTCGCGGCGGGGACAGCCAGATTCGGGTCGAGATCTATTCCCGCACGCGTGGCGGAGAGTTCTGCCGACACGCCACGGCCAAGGTTGAACAATCGCCGCGCGAATGTGCGCACGCGCACCCGGAAGCCCAAGGTCCCGCCACCGGGACAACAGTGTCGCCGGCCGATTTTTATGCCCTGCTCCGCCAAACCGGCCAACACCATGGTCCGGCGTTCGCGGCCTTAAGCCGGATCGTGCGCCTGGCCGATGGTTCCGCGGAAACCGAGATCAGCATTCCCGACGAGGCGCCGCGCCATCCCGGGTATCGGCTGCACCCCGTGGTATTGGATGCGGCATTGCAAAGCGTGGGTGCCGCGATACCCGACGGCGAGATCGCGGGGTCGGCGGAAGCCAGCTATCTGCCAGTGTCGTTCGAGACCATCCGGGTGTACCGCGACATCGGTCGGCACGTCAGGTGTCGTGCCCACCTGACAAACCTCGACGGCGGCACCGGAAAGATGGGCAGGATCGTCCTAATCAACGACGCCGGCCACATAGCGGCCGAAGTGGACGGCATCTATCTGCGTCGTGTCGAACGCCGTGCGGTACCCCTGCCACTAGAGCAGAAGATCTTCGATGCCGAATGGACCGAAAGCCCGATCGCAGCCGTGCCGGCTCCGGAGCCAGCTGCCGAGACGACGCGGGGAAGTTGGCTGGTACTCGCCGATGCAACGGTGGATGCGCCAGGCAAGGCCCAGGCCAAGTCGATGGCCGACGACTTCGTGCAGCAGTGGCGCTCACCGATGCGGCGGGTGCACACCGCCGATATCCACGACGAATCGGCGGTGCTGGCCGCATTTGCAGAAACGGCAGGCGATCCCGAGCACCCGCCGGTTGGCGTGGTGGTGTTCGTCGGCGGTGCCTCGAGTCGACTGGACGACGAGCTGGCGGCGGCGCGCGACACGGTGTGGTCGATCACCACGGTGGTTCGTGCGGTCGTCGGCACGTGGCACGGCCGATCACCGCGGCTATGGCTGGTCACCGGGGGCGGACTTTCCGTTGCCGACGACGAGCCGGGAACACCCGCGGCGGCTTCCTTGAAAGGGCTGGTGCGGGTGCTCGCCTTCGAGCACCCGGACATGCGCACCACCCTGGTCGATCTGGACATCACACAAGACCCGCTGACCGCGCTGAGCGCGGAACTGCGGAATGCCGGGAGTGGGTCGCGCCATGATGACGTGATCGCGTGGCGCGGCGAGCGCAGGTTCGTCGAACGGCTGTCGCGCGCCACGATCGATGTATCCAAAGGGCATCCGGTGGTGCGCCAGGGAGCGTCGTACGTCGTCACCGGCGGCCTCGGCGGTCTCGGCCTGGTCGTCGCTCGTTGGCTGGTGGACCGCGGCGCCGGCCGGGTGGTGCTGGGTGGCCGCAGCGATCCCACTGACGAGCAGTGCAACGTCCTGGCCGAACTGCAGACCCGCGCCGAGATCGTGGTTGTCCGTGGCGACGTGGCATCGCCGGGGGTGGCAGAAAAGCTGATTGAGACGGCCCGACAGTCTGGGGGCCAATTGCGCGGCGTCGTGCACGCCGCCGCGGTCATCGAAGACAGCCTGGTGTTCTCTATGAGCAGGGACAACCTAGAACGGGTGTGGGCACCCAAGGCCACCGGTGCGCTGCGCATGCACGAAGCCACCGCTGACTGCGAGCTCGACTGGTGGCTCGGATTCTCTTCCGCCGCTTCGCTATTGGGTTCTCCCGGGCAAGCGGCCTACGCGTGCGCCAGCGCGTGGCTGGACGCGCTGGTCGGATGGCGCAGGGCATCCGGCCTGCCGGCCGCGGTGATCAACTGGGGTCCGTGGTCGGAGGTAGGCGTCGCCCAGGCCTTGGTGGGCAGTGTTCTCGACACGATCAGTGTCGCAGAAGGCATCGAGGCTCTCGACTCATTGCTTGCCGCCGACCGGATCCGCACTGGAGTGGCTCGGCTGCGTGCCGATCGGGCCCTGGTCGCATTCCCGGAGATCCGCAGCATCAGCTACTTCACCCAGGTGGTCGAGGAGCTGGACTCGGCGGGTGACCTCGGCGACTGGGGCGGGCCCGACGCGCTTGCCGACCTCGACCCGGGCGAGGCGCGGCGCGCGGTGACCGAGCGGATGTGTGCGCGCATCGCTGCGGTGATGGGCTACACTGACCAGTCGACTGTCGAACCCGCCGTGCCCTTGGACAAGCCCCTGACCGAGCTGGGGCTGGATTCTCTGATGGCGGTACGAATACGCAACGGCGCGCGGGCGGATTTCGGCGTGGAACCGCCGGTAGCGCTGATACTGCAAGGCGCGTCCTTGCATGACCTGACGGCGGACTTAATGCGCCAACTCGGGCTCAATGATCCCGATCCGGCGCTCAACAACGCTGACACTATTCGCGACCGGGCGCGCCAGCGCGCGGCAGCGCGACACGGAGCCGCGATGCGGCGCCGACCTAAACCTGAAGTACAGGGAGGATAA
