| Accession | ARO:3002955 |
| Synonym(s) | vanY-A vanYA |
| CARD Short Name | vanY_in_vanA_cl |
| Definition | Also known as vanYA, is a vanY variant found in the vanA gene cluster. |
| AMR Gene Family | glycopeptide resistance gene cluster, vanY |
| Drug Class | glycopeptide antibiotic |
| Resistance Mechanism | antibiotic target alteration |
| Resistomes with Perfect Matches | Enterococcus faecalisp+wgs, Enterococcus faeciump+wgs, Klebsiella pneumoniaewgs, Staphylococcus aureuswgs |
| Resistomes with Sequence Variants | Bacillus anthracisg+wgs, Bacillus cereusg+p+wgs, Bacillus pumiluswgs, Bacillus subtiliswgs, Bacillus thuringiensisg+p+wgs, Borreliella afzeliig, Borreliella gariniig+wgs, Brevibacillus brevisg+wgs, Brevibacillus laterosporusg+wgs+gi, Enterococcus aviump, Enterococcus faecalisp+wgs, Enterococcus faeciumg+p+wgs, Glutamicibacter creatinolyticusg, Herbinix luporumg+wgs, Klebsiella pneumoniaewgs, Lactococcus garvieaeg+wgs, Leclercia adecarboxylatawgs, Macrococcus canisg+wgs, Micrococcus luteusg+wgs, Paenibacillus mucilaginosuswgs, Parvimonas micrag+wgs, Pseudomonas putidawgs, Pseudomonas stutzeriwgs, Rhodopseudomonas palustrisg+wgs, Salmonella entericawgs, Staphylococcus aureusg+p+wgs, Staphylococcus capitiswgs, Staphylococcus epidermidiswgs, Staphylococcus equorumwgs, Staphylococcus haemolyticusg+wgs, Staphylococcus simulanswgs, Streptococcus agalactiaewgs, Streptococcus constellatuswgs, Streptococcus cristatuswgs, Streptococcus gordoniiwgs, Streptococcus sanguinisg+wgs, Streptococcus uberiswgs, Treponema pallidumwgs, Vibrio vulnificuswgs |
| 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) Arthur M, et al. 1993. J Bacteriol 175(1): 117-127. Characterization of Tn1546, a Tn3-related transposon conferring glycopeptide resistance by synthesis of depsipeptide peptidoglycan precursors in Enterococcus faecium BM4147. (PMID 8380148) |
Prevalence of vanY gene in vanA 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 anthracis | 100% | 0% | 78.07% | 0% |
| Bacillus cereus | 66.67% | 3.04% | 37.99% | 0% |
| Bacillus pumilus | 0% | 0% | 0.56% | 0% |
| Bacillus subtilis | 0% | 0% | 0.29% | 0% |
| Bacillus thuringiensis | 66.25% | 1.31% | 61.08% | 0% |
| Borreliella afzelii | 57.58% | 0% | 0% | 0% |
| Borreliella garinii | 90.14% | 0% | 9.52% | 0% |
| Brevibacillus brevis | 100% | 0% | 100% | 0% |
| Brevibacillus laterosporus | 83.33% | 0% | 64.71% | 100% |
| Enterococcus avium | 0% | 33.33% | 0% | 0% |
| Enterococcus faecalis | 0% | 2.71% | 6.24% | 0% |
| Enterococcus faecium | 0.96% | 9.97% | 28.1% | 0% |
| Escherichia coli | 0% | 0% | 0% | 0% |
| Glutamicibacter creatinolyticus | 100% | 0% | 0% | 0% |
| Herbinix luporum | 100% | 0% | 100% | 0% |
| Klebsiella pneumoniae | 0% | 0% | 0.01% | 0% |
| Lactococcus garvieae | 5.56% | 0% | 4.44% | 0% |
| Leclercia adecarboxylata | 0% | 0% | 2.33% | 0% |
| Macrococcus canis | 100% | 0% | 100% | 0% |
| Micrococcus luteus | 16.67% | 0% | 21.11% | 0% |
| Paenibacillus mucilaginosus | 0% | 0% | 50% | 0% |
| Parvimonas micra | 30% | 0% | 18.75% | 0% |
| Pseudomonas putida | 0% | 0% | 0.53% | 0% |
| Pseudomonas stutzeri | 0% | 0% | 0.76% | 0% |
| Rhodopseudomonas palustris | 7.69% | 0% | 11.11% | 0% |
| Salmonella enterica | 0% | 0% | 0.01% | 0% |
| Staphylococcus aureus | 0.7% | 0.19% | 0.13% | 0% |
| Staphylococcus capitis | 0% | 0% | 0.63% | 0% |
| Staphylococcus epidermidis | 0% | 0% | 0.5% | 0% |
| Staphylococcus equorum | 0% | 0% | 3.57% | 0% |
| Staphylococcus haemolyticus | 17.24% | 0% | 17.58% | 0% |
| Staphylococcus simulans | 0% | 0% | 3.39% | 0% |
| Streptococcus agalactiae | 0% | 0% | 0.13% | 0% |
| Streptococcus constellatus | 0% | 0% | 4.55% | 0% |
| Streptococcus cristatus | 0% | 0% | 2.86% | 0% |
| Streptococcus gordonii | 0% | 0% | 1.28% | 0% |
| Streptococcus sanguinis | 14.29% | 0% | 8.25% | 0% |
| Streptococcus uberis | 0% | 0% | 0.89% | 0% |
| Treponema pallidum | 0% | 0% | 11.11% | 0% |
| Vibrio vulnificus | 0% | 0% | 0.41% | 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