patB

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Accession	ARO:3000025
CARD Short Name	patB
Definition	PatB is an ABC transporter of Streptococcus pneumoniae that interacts with PatA to confer fluoroquinolone resistance..
AMR Gene Family	ATP-binding cassette (ABC) antibiotic efflux pump
Drug Class	fluoroquinolone antibiotic
Resistance Mechanism	antibiotic efflux
Efflux Component	efflux pump complex or subunit conferring antibiotic resistance
Resistomes with Perfect Matches	Streptococcus pneumoniae^g+wgs
Resistomes with Sequence Variants	Streptococcus agalactiae^wgs, Streptococcus canis^g+wgs, Streptococcus cristatus^g+wgs, Streptococcus dysgalactiae^g+p+wgs, Streptococcus equi^g+wgs, Streptococcus gordonii^g+wgs, Streptococcus gwangjuense^g+wgs, Streptococcus iniae^g+wgs, Streptococcus mitis^g+wgs, Streptococcus pneumoniae^g+wgs, Streptococcus porcinus^g+wgs, Streptococcus pseudopneumoniae^g+wgs, Streptococcus pseudoporcinus^g+wgs, Streptococcus pyogenes^g+wgs, Streptococcus sanguinis^g+wgs, Streptococcus suis^g+wgs, Streptococcus uberis^g+wgs
Classification	10 ontology terms \| Show + process or component of antibiotic biology or chemistry + mechanism of antibiotic resistance + determinant of antibiotic resistance + antibiotic molecule + antibiotic efflux [Resistance Mechanism] + efflux pump complex or subunit conferring antibiotic resistance [Efflux Component] + fluoroquinolone antibiotic [Drug Class] + norfloxacin [Antibiotic] + ATP-binding cassette (ABC) antibiotic efflux pump [AMR Gene Family] + ciprofloxacin [Antibiotic]
Parent Term(s)	2 ontology terms \| Show + subunit of efflux pump conferring antibiotic resistance + part_of PatA-PatB
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 414 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)

Species	NCBI Chromosome	NCBI Plasmid	NCBI WGS	NCBI GI	GRDI-AMR2
Streptococcus agalactiae	0%	0%	0.06%	0%	0%
Streptococcus agalactiae	0%	0%	0%	0%	0%
Streptococcus canis	0%	0%	0%	0%	0%
Streptococcus canis	100%	0%	100%	0%	0%
Streptococcus cristatus	100%	0%	100%	0%	0%
Streptococcus cristatus	0%	0%	0%	0%	0%
Streptococcus dysgalactiae	98%	6.25%	99.07%	0%	0%
Streptococcus dysgalactiae	0%	0%	0%	0%	0%
Streptococcus equi	100%	0%	100%	0%	0%
Streptococcus equi	0%	0%	0%	0%	0%
Streptococcus gordonii	0%	0%	0%	0%	0%
Streptococcus gordonii	100%	0%	98.72%	0%	0%
Streptococcus gwangjuense	0%	0%	0%	0%	0%
Streptococcus gwangjuense	100%	0%	100%	0%	0%
Streptococcus iniae	0%	0%	0%	0%	0%
Streptococcus iniae	100%	0%	89.53%	0%	0%
Streptococcus mitis	0%	0%	0%	0%	0%
Streptococcus mitis	100%	0%	99.49%	0%	0%
Streptococcus pneumoniae	100%	0%	99.81%	0%	0%
Streptococcus pneumoniae	3.4%	0%	2.44%	0%	0%
Streptococcus porcinus	100%	0%	100%	0%	0%
Streptococcus porcinus	0%	0%	0%	0%	0%
Streptococcus pseudopneumoniae	100%	0%	100%	0%	0%
Streptococcus pseudopneumoniae	0%	0%	0%	0%	0%
Streptococcus pseudoporcinus	100%	0%	100%	0%	0%
Streptococcus pseudoporcinus	0%	0%	0%	0%	0%
Streptococcus pyogenes	0%	0%	0%	0%	0%
Streptococcus pyogenes	100%	0%	99.64%	0%	0%
Streptococcus sanguinis	0%	0%	0%	0%	0%
Streptococcus sanguinis	100%	0%	100%	0%	0%
Streptococcus suis	0%	0%	0%	0%	0%
Streptococcus suis	100%	0%	99.42%	0%	0%
Streptococcus uberis	100%	0%	100%	0%	0%
Streptococcus uberis	0%	0%	0%	0%	0%

Show Perfect Only

Detection Models

protein homolog model

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

Protein
DNA

>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

Curator Acknowledgements

Curator	Description	Most Recent Edit

patB

Prevalence: protein homolog model (view sequences)

Graph