| Accession | MO:0000002 | ||
| Definition | The protein variant model is an AMR detection model. Protein variant models are similar to protein homolog models - they detect the presence of a protein sequence based on its similarity to a curated reference sequence, but secondarily search submitted query sequences for curated sets of mutations shown clinically to confer resistance relative to wild-type. This model includes a protein reference sequence, a curated BLASTP cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of: single resistance variants, insertions, deletions, co-dependent resistance variants, nonsense SNPs, and/or frameshift mutations. Protein variant model matches to reference sequences are categorized on two criteria: strict and loose. A strict match has a BLASTP bitscore above the curated BLASTP cutoff value and contains at least one detected mutation from amongst the mapped resistance variants; a loose match has a BLASTP bitscore below the curated BLASTP cutoff value but still contains at least one detected mutation from amongst the mapped resistance variants. Regardless of BLASTP bitscore, if a sequence does not contain one of the mapped resistance variants, it is not considered a match and not detected by the protein variant model. | ||
| Classification | 1 ontology terms | Show | ||
| Parent Term(s) | 1 ontology terms | Show | ||
| Sub-Term(s) | 21 ontology terms | Show + single resistance variant part_of + BLASTP e-value 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 | ||
| Model List |
|