| Accession | ARO:3002958 |
| Synonym(s) | vanY-F vanYF |
| CARD Short Name | vanY_in_vanF_cl |
| Definition | Also known as vanYF, is a vanY variant found in the vanF gene cluster. |
| AMR Gene Family | glycopeptide resistance gene cluster, vanY |
| Drug Class | glycopeptide antibiotic |
| Resistance Mechanism | antibiotic target alteration |
| Resistomes with Sequence Variants | Bacillus amyloliquefacienswgs, Bacillus anthracisg+wgs, Bacillus cereusg+p+wgs, Bacillus pumiluswgs, Bacillus subtiliswgs, Bacillus thuringiensisg+p+wgs, Bacillus velezensiswgs, Blautia productag+wgs, Brevibacillus brevisg+wgs, Brevibacillus laterosporusg+wgs, Clostridium botulinumg+wgs, Clostridium sporogenesg, Erysipelatoclostridium ramosumg+wgs, Faecalibacterium prausnitziig+wgs, Kocuria palustriswgs, Lactococcus garvieaewgs, Macrococcus caniswgs, Micrococcus luteusg+wgs, Pseudomonas fluorescensp, Rothia mucilaginosag+wgs, Staphylococcus aureuswgs, Staphylococcus epidermidiswgs, Staphylococcus massiliensiswgs, Staphylococcus pasteurig+wgs, Staphylococcus warnerig+wgs, Streptococcus agalactiaewgs, Streptococcus iniaeg+wgs, Streptococcus intermediuswgs, Streptococcus pyogeneswgs, Streptococcus sobrinusg+wgs, Streptococcus uberisg+wgs |
| Classification | 12 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] + vancomycin [Antibiotic] |
| Parent Term(s) | 2 ontology terms | Show |
| Publications | Fraimow H, et al. 2005. Antimicrob Agents Chemother 49(7): 2625-2633. Putative VanRS-like two-component regulatory system associated with the inducible glycopeptide resistance cluster of Paenibacillus popilliae. (PMID 15980329) |
Prevalence of vanY gene in vanF 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 |
|---|---|---|---|---|
| Bacillus amyloliquefaciens | 0% | 0% | 1.12% | 0% |
| Bacillus anthracis | 100% | 0% | 77.63% | 0% |
| Bacillus cereus | 89.25% | 2.13% | 76.87% | 0% |
| Bacillus pumilus | 0% | 0% | 1.12% | 0% |
| Bacillus subtilis | 0% | 0% | 0.29% | 0% |
| Bacillus thuringiensis | 55% | 0.07% | 55.15% | 0% |
| Bacillus velezensis | 0% | 0% | 0.37% | 0% |
| Blautia producta | 33.33% | 0% | 36.36% | 0% |
| Brevibacillus brevis | 85.71% | 0% | 50% | 0% |
| Brevibacillus laterosporus | 83.33% | 0% | 76.47% | 0% |
| Clostridium botulinum | 23.88% | 0% | 13.04% | 0% |
| Clostridium sporogenes | 8.33% | 0% | 0% | 0% |
| Erysipelatoclostridium ramosum | 100% | 0% | 51.16% | 0% |
| Faecalibacterium prausnitzii | 26.67% | 0% | 12.62% | 0% |
| Kocuria palustris | 0% | 0% | 66.67% | 0% |
| Lactococcus garvieae | 0% | 0% | 6.67% | 0% |
| Macrococcus canis | 0% | 0% | 50% | 0% |
| Micrococcus luteus | 22.22% | 0% | 2.22% | 0% |
| Pseudomonas fluorescens | 0% | 11.11% | 0% | 0% |
| Rothia mucilaginosa | 20% | 0% | 15.79% | 0% |
| Staphylococcus aureus | 0% | 0% | 0.01% | 0% |
| Staphylococcus epidermidis | 0% | 0% | 0.42% | 0% |
| Staphylococcus massiliensis | 0% | 0% | 57.14% | 0% |
| Staphylococcus pasteuri | 87.5% | 0% | 96.15% | 0% |
| Staphylococcus warneri | 83.33% | 0% | 64.75% | 0% |
| Streptococcus agalactiae | 0% | 0% | 0.06% | 0% |
| Streptococcus iniae | 100% | 0% | 98.84% | 0% |
| Streptococcus intermedius | 0% | 0% | 2.27% | 0% |
| Streptococcus pyogenes | 0% | 0% | 0.1% | 0% |
| Streptococcus sobrinus | 100% | 0% | 97.96% | 0% |
| Streptococcus uberis | 25% | 0% | 0.89% | 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