patB

Accession ARO:3000025
CARD Short NamepatB
DefinitionPatB is an ABC transporter of Streptococcus pneumoniae that interacts with PatA to confer fluoroquinolone resistance..
AMR Gene FamilyATP-binding cassette (ABC) antibiotic efflux pump
Drug Classfluoroquinolone antibiotic
Resistance Mechanismantibiotic efflux
Efflux Componentefflux pump complex or subunit conferring antibiotic resistance
Resistomes with Perfect MatchesStreptococcus pneumoniaeg+wgs
Resistomes with Sequence VariantsKlebsiella pneumoniaewgs, Pseudomonas aeruginosawgs, Streptococcus agalactiaewgs, Streptococcus canisg+wgs, Streptococcus cristatusg+wgs, Streptococcus dysgalactiaeg+p+wgs, Streptococcus equig+wgs, Streptococcus gordoniig+wgs, Streptococcus gwangjuenseg, Streptococcus iniaeg+wgs, Streptococcus mitisg+wgs, Streptococcus pneumoniaeg+wgs, Streptococcus porcinusg+wgs, Streptococcus pseudopneumoniaeg+wgs, Streptococcus pseudoporcinusg+wgs, Streptococcus pyogenesg+wgs, Streptococcus sanguinisg+wgs, Streptococcus suisg+wgs, Streptococcus uberisg+wgs
Classification10 ontology terms | Show
Parent Term(s)2 ontology terms | Show
Publications

El Garch F, et al. 2010. J Antimicrob Chemother 65(10): 2076-2082. Fluoroquinolones induce the expression of patA and patB, which encode ABC efflux pumps in Streptococcus pneumoniae. (PMID 20709735)

Garvey MI, et al. 2010. Antimicrob Agents Chemother 55(1): 190-196. Overexpression of patA and patB, which encode ABC transporters, is associated with fluoroquinolone resistance in clinical isolates of Streptococcus pneumoniae. (PMID 20937787)

Resistomes

Prevalence of patB among the sequenced genomes, plasmids, and whole-genome shotgun assemblies available at NCBI or IslandViewer for 377 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).

Prevalence: protein homolog model (view sequences)

SpeciesNCBI ChromosomeNCBI PlasmidNCBI WGSNCBI GI
Klebsiella pneumoniae0%0%0.02%0%
Pseudomonas aeruginosa0%0%0.02%0%
Streptococcus agalactiae0%0%0.07%0%
Streptococcus canis100%0%100%0%
Streptococcus cristatus100%0%100%0%
Streptococcus dysgalactiae100%7.69%59.79%0%
Streptococcus equi100%0%75.4%0%
Streptococcus gordonii100%0%71.83%0%
Streptococcus gwangjuense100%0%0%0%
Streptococcus iniae100%0%89.53%0%
Streptococcus mitis100%0%86.45%0%
Streptococcus pneumoniae100%0%95.49%0%
Streptococcus porcinus100%0%100%0%
Streptococcus pseudopneumoniae100%0%76.07%0%
Streptococcus pseudoporcinus100%0%100%0%
Streptococcus pyogenes100%0%21.06%0%
Streptococcus sanguinis100%0%59.04%0%
Streptococcus suis100%0%80.54%0%
Streptococcus uberis100%0%41.9%0%
Show Perfect Only


Detection Models

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): 750


>gb|AAK76136.1|-|patB [Streptococcus pneumoniae TIGR4]
MKTVQFFWHYFKVYKFSFVVVILMIVLATFAQALFPVFSGQAVTQLANLVQAYQNGNPELVWQSLSGIMVNLGLLVLVLFISSVIYMCLM
TRVIAESTNEMRKGLFGKLAQLTVSFFDRRQDGDILSHFTSDLDNILQAFNESLIQVMSNIVLYIGLILVMFSRNVTLALITIASTPLAF
LMLIFIVKMARKYTNLQQKEVGKLNAYMDESISGQKAVIVQGIQEDMMAGFLEQNERVRKATFKGRMFSGILFPVMNGMSLINTAIVIFA
GSAVLLNDKSIETSTALGLIVMFAQFSQQYYQPIIQVAASWGSLQLAFTGAERIQEMFDAEEEIRPEKAPTFTKLQESVEISHIVFSYLP
DKPILKDVSISAPKGQMTAVVGPTGSGKTTIMNLINRFYDVDAGGIYFDGKDIRGYDLDSLRSKVGIVLQDSVLFSGTIRDNIRFGVPDA
SQEMVEVAAKATHIHDYIESLPDKYDTLIDDDQSIFSTGQKQLISIARTLMTDPEVLILDEATSNVDTVTESKIQHAMEVVVAGRTSFVI
AHRLKTILNADQIIVLKDGEVIERGNHHELLKLGGFYSELYHNQFVFE


>gb|AE005672.3|-|1980558-1982324|patB [Streptococcus pneumoniae TIGR4]
ATGAAGACAGTTCAATTTTTTTGGCATTATTTTAAGGTCTACAAGTTCTCATTTGTAGTTGTCATCCTGATGATTGTTCTGGCGACTTTT
GCCCAAGCCCTCTTTCCAGTCTTTTCTGGACAAGCGGTGACGCAGCTAGCCAATTTAGTTCAAGCTTATCAAAATGGCAATCCAGAACTT
GTATGGCAAAGCCTATCAGGAATCATGGTCAATCTTGGCCTGCTGGTTTTGGTTCTATTTATCTCTAGTGTAATATACATGTGTCTCATG
ACGCGCGTGATTGCAGAATCGACCAACGAGATGCGCAAAGGCCTCTTTGGTAAGCTTGCTCAGTTGACGGTTTCTTTCTTTGACCGTCGA
CAAGATGGCGATATCCTGTCTCATTTTACCAGTGATTTGGATAATATCCTCCAAGCCTTTAACGAAAGCTTGATTCAGGTCATGAGCAAT
ATTGTTTTATACATTGGTCTGATTCTTGTCATGTTTTCGAGAAATGTGACGCTGGCTCTCATCACCATTGCCAGCACCCCATTGGCTTTC
CTTATGCTGATTTTCATCGTGAAAATGGCACGCAAATACACCAACCTCCAGCAGAAAGAGGTAGGGAAGCTCAACGCCTATATGGATGAG
AGCATCTCAGGCCAAAAAGCCGTGATTGTGCAAGGAATTCAAGAGGATATGATGGCAGGATTTCTTGAACAAAATGAGCGCGTGCGCAAG
GCAACCTTTAAAGGAAGAATGTTCTCAGGAATTCTTTTCCCTGTCATGAATGGGATGAGCCTGATTAATACAGCCATCGTCATCTTTGCT
GGTTCGGCTGTACTTTTGAATGATAAGTCTATTGAAACAAGTACAGCCCTAGGTTTGATTGTTATGTTTGCACAATTTTCACAGCAGTAC
TACCAGCCTATTATCCAAGTTGCAGCGAGTTGGGGAAGCCTTCAGTTGGCCTTTACTGGAGCTGAACGAATTCAGGAAATGTTTGATGCA
GAGGAGGAAATCCGACCTGAAAAGGCTCCAACCTTCACTAAGTTGCAAGAAAGTGTTGAAATCAGTCATATCGTTTTTTCATACTTGCCT
GATAAACCTATTTTGAAAGATGTCAGCATTTCTGCCCCTAAAGGCCAGATGACAGCAGTTGTTGGGCCGACAGGTTCAGGAAAAACGACT
ATTATGAACCTCATCAATCGCTTTTATGATGTTGATGCTGGTGGTATTTATTTTGATGGTAAAGACATTCGTGGCTATGACTTAGATAGT
CTTAGAAGCAAGGTGGGAATTGTATTGCAAGATTCGGTCTTGTTTAGCGGAACGATTAGAGACAATATCCGATTTGGTGTGCCAGATGCT
AGTCAGGAAATGGTTGAGGTAGCAGCAAAAGCAACCCACATTCACGACTATATCGAAAGTTTGCCTGATAAGTACGATACTCTTATTGAT
GATGACCAGAGCATCTTTTCAACAGGGCAGAAGCAATTGATTTCAATCGCTCGAACCCTGATGACAGATCCAGAAGTTCTCATTCTCGAT
GAAGCAACTTCAAACGTAGATACGGTGACAGAAAGCAAGATTCAGCATGCCATGGAGGTGGTTGTAGCAGGTAGAACTAGTTTCGTCATT
GCCCACCGCTTGAAAACCATTCTCAATGCAGATCAGATTATTGTCCTTAAAGATGGAGAAGTCATTGAACGTGGTAACCACCATGAACTT
TTGAAGCTAGGTGGCTTTTATTCAGAACTCTATCACAATCAATTTGTTTTCGAATAA