pmpM (PA1361, Q9I3Y3) notes

Review session 2026-11-05 (PseudoCAP IBA-seed protocol, tier 2)

Fetched with just fetch-gene PSEAE Q9I3Y3 --alias pmpM; accession matches the worklist.
Reviewed (Swiss-Prot) entry. No deep-research provider; PubMed and Europe PMC searches failed
(HTTP 500/503) during the session. The seed paper PMID:14679249 is cached with full text and
was read in full.

Literature

PMID:14679249 (He et al. 2004), full text: pmpM cloned into drug-hypersensitive E. coli KAM32
raises MICs of fluoroquinolones, benzalkonium chloride, ethidium, TPP and others;
energy-dependent ethidium efflux is Na+-independent; in everted membrane vesicles benzalkonium
drives H+ efflux PMID:14679249. Deleting
pmpM in the Mex-deficient strain PMX52 lowers MICs of benzalkonium, ethidium, acriflavine and
TPPCl. No localization, fractionation or topology experiment is reported; the only
membrane-related data are transport assays in E. coli everted membrane vesicles.
UniProt Q9I3Y3: MATE family (TIGR00797, PF01554 x2), 12 predicted transmembrane helices;
Swiss-Prot location cell inner membrane, multi-pass (ECO:0000250).

Annotation decisions

GO:0005886 plasma membrane (IDA, IEA): ACCEPT. The IDA rests on H+/drug antiport measured in
everted (inner) membrane vesicles of E. coli expressing pmpM; together with 12 TM helices.
GO:0098567 periplasmic side of plasma membrane (IDA): REMOVE, PSEUDOCAP WRONG_TERM defect
(CONFIRMED; full text read).
GO:0016020 membrane (IBA, IEA): TOO_GENERAL (plasma membrane accepted, is_a membrane).
GO:0042910 xenobiotic transmembrane transporter activity (IBA, IEA): ACCEPT.
GO:0015297 antiporter activity (IEA): MODIFY to GO:0140968 polyspecific organic
cation:proton antiporter activity (substrates are organic cations; H+ coupling shown).
GO:0042908 xenobiotic transport (IEA): MODIFY to GO:1990961 xenobiotic detoxification by
transmembrane export across the plasma membrane.
GO:0055085 transmembrane transport (IEA): TOO_GENERAL (GO:1990961 in core_functions entails it).
GO:0046677 response to antibiotic (IBA): KEEP_AS_NON_CORE.
Action counts: ACCEPT 4, MODIFY 2, TOO_GENERAL 3, KEEP_AS_NON_CORE 1, REMOVE 1.

PseudoCAP IBA-seed assessment

PTN node	node term	n_seeds	leaf IBAs	seed annotation (term, evidence, PMID)	verdict	rationale	other seeds	IBD stands without this seed?
PTN000129144	GO:0016020 membrane	19	2231 (102 taxa)	GO:0005886 plasma membrane, IDA, PMID:14679249	SOUND	H+/benzalkonium antiport measured in everted inner-membrane vesicles of E. coli expressing pmpM; a membrane location of the transporter follows, and the node term is broader still.	18 others: E. coli MdtK (P37340), human MATE1/MATE2-K (Q96FL8, Q86VL8), mouse and rat MATEs, 12 Arabidopsis DTX/MATE proteins	Yes
PTN000129144	GO:0016020 membrane	19	2231 (102 taxa)	GO:0098567 periplasmic side of plasma membrane, IDA, PMID:14679249	WRONG	No sidedness or topology experiment in the paper; PmpM is a 12-helix integral membrane protein spanning both leaflets. The row adds nothing the plasma membrane row does not, and its term is wrong.	as above	Yes

The membrane IBD at the MATE-family root (2231 leaves) is supported by many independent
experimental seeds across bacteria, plants and mammals, and membrane is a term that suits every
MATE transporter. No GO_CENTRAL defect. One PSEUDOCAP defect (GO:0098567, CONFIRMED).