Literature as in genes/PSEAE/pvdR/pvdR-notes.md (same four PvdRT-OpmQ papers;
PMID:19906986 full text read, the others abstract only). OpmQ is the OMF lipoprotein
PMID:19906986.
Other seeds' experimental support queried live in QuickGO on 2026-11-05.
| PTN node | node term | n_seeds | leaf IBAs | seed annotation (term, evidence, PMID) | verdict | rationale | other seeds | IBD stands without this seed? |
|---|---|---|---|---|---|---|---|---|
| PTN008411811 | GO:0016020 membrane | 3 | 85 (20 taxa) | GO:1990281 efflux pump complex, IDA PMID:19906986/21035449/22187978; IMP PMID:19906986/22187978/23766114 | SOUND | OpmQ is the outer-membrane component of the pump; a membrane protein complex term is valid evidence for membrane. PMID:19906986 IDA code wrong (mutants only) -> PSEUDOCAP WRONG_EVIDENCE_CODE, PROBABLE. | OprM Q51487 (cell outer membrane EXP PMID:10889211; efflux pump complex IDA), OprJ Q51397 (outer membrane IDA PMID:8878035) | Yes |
| PTN008411811 | GO:0022857 transmembrane transporter activity | 4 | 85 (20 taxa) | GO:0015562 efflux transmembrane transporter activity, same six rows | SOUND | Pump exports PVD; GO:0015562 is_a GO:0022857. Same IDA-code defect. | OprM (GO:0015562 IDA/IMP), OprJ (GO:0022857 IMP/IGI), E. coli CusC P77211 (GO:0005375 IGI) | Yes |
Node terms are generic and suit an OMF clade. No GO_CENTRAL defect. The leaf IBAs on
OpmQ are TOO_GENERAL (membrane, transporter activity) or MODIFY (transmembrane
transport -> GO:0015891 siderophore transport, with propagation_review
NO_FAILURE_CORE).
PvdR (PA2389) shares the operon and the same PseudoCAP rows; it seeds PTN001253051.
The GO:0002049 IMP (PMID:12686626) gets the same MODIFY and PSEUDOCAP WRONG_TERM
defect as on pvdR.