| Accession | ARO:3002957 |
| Synonym(s) | vanY-D vanYD |
| CARD Short Name | vanY_in_vanD_cl |
| Definition | Also known as vanYD, is a vanY variant found in the vanD gene cluster. |
| AMR Gene Family | glycopeptide resistance gene cluster, vanY |
| Drug Class | glycopeptide antibiotic |
| Resistance Mechanism | antibiotic target alteration |
| Resistomes with Sequence Variants | Blautia productawgs, Enterococcus faecalisg+wgs, Enterococcus faeciumg+wgs, Ruthenibacterium lactatiformanswgs |
| Classification | 13 ontology terms | Show + process or component of antibiotic biology or chemistry + mechanism of antibiotic resistance + antibiotic target alteration [Resistance Mechanism] + restructuring of bacterial cell wall conferring antibiotic resistance + determinant of antibiotic resistance + antibiotic molecule + glycopeptide antibiotic [Drug Class] + protein(s) conferring antibiotic resistance via molecular bypass + antibiotic resistance gene cluster, cassette, or operon + gene(s) or protein(s) associated with a glycopeptide resistance cluster + glycopeptide resistance gene cluster [AMR Gene Family] + teicoplanin [Antibiotic] + vancomycin [Antibiotic] |
| Parent Term(s) | 2 ontology terms | Show |
| Publications | Courvalin P. 2005. Clin Infect Dis 42(SUPPL 1): S25-S34. Vancomycin resistance in gram-positive cocci. (PMID 16323116) Depardieu F, et al. 2002. Antimicrob Agents Chemother 47(1): 7-18. VanD-type vancomycin-resistant Enterococcus faecium 10/96A. (PMID 12499162) |
Prevalence of vanY gene in vanD cluster among the sequenced genomes, plasmids, and whole-genome shotgun assemblies available at NCBI or IslandViewer for 413 important pathogens (see methodological details and complete list of analyzed pathogens). Values reflect percentage of genomes, plasmids, genome islands, or whole-genome shotgun assemblies that have at least one hit to the AMR detection model. Default view includes percentages calculated based on Perfect plus Strict RGI hits. Select the checkbox to view percentages based on only Perfect matches to AMR reference sequences curated in CARD (note: this excludes resistance via mutation as references in protein variant models are often wild-type, sensitive sequences).
| Species | NCBI Chromosome | NCBI Plasmid | NCBI WGS | NCBI GI |
|---|---|---|---|---|
| Blautia producta | 0% | 0% | 27.27% | 0% |
| Enterococcus faecalis | 0.91% | 0% | 0.04% | 0% |
| Enterococcus faecium | 0.96% | 0% | 0.31% | 0% |
| Ruthenibacterium lactatiformans | 0% | 0% | 3.33% | 0% |
Model Type: protein homolog model
Model Definition: Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.
Bit-score Cut-off (blastP): 50