| Accession | MO:0000002 | ||
| 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. | ||
| Classification | 1 ontology terms | Show | ||
| Parent Term(s) | 1 ontology terms | Show | ||
| Sub-Term(s) | 20 ontology terms | Show + single resistance variant part_of + multiple resistance variants part_of + nonsense mutation part_of + co-dependent single resistance variant part_of + frameshift mutation part_of + co-dependent nonsense SNP part_of + co-dependent insertion/deletion part_of + BLASTN bit-score part_of + BLASTP bit-score part_of + snp in promoter region part_of + high confidence TB part_of + moderate confidence TB part_of + minimal confidence TB part_of + no association with resistance TB part_of + indeterminate confidence TB part_of + disruptive mutation in regulatory element part_of + insertion mutation from peptide sequence part_of + insertion mutation from nucleotide sequence part_of + deletion mutation from peptide sequence part_of + deletion mutation from nucleotide sequence part_of | ||
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