OpmQ (PA2391) is the outer-membrane factor (OMF, TolC/NodT family lipoprotein) of the tripartite ATP-binding cassette efflux pump PvdRT-OpmQ, which also contains the inner-membrane ABC transporter PvdT and the periplasmic membrane fusion protein PvdR. OpmQ provides the outer-membrane exit channel through which the pump moves the siderophore pyoverdine from the periplasm to the extracellular medium. The pump secretes newly made pyoverdine, recycles pyoverdine after iron release from ferri-pyoverdine taken up by FpvA, and expels pyoverdine complexed with non-iron metals. opmQ mutants accumulate pyoverdine in the periplasm. Expression is iron-regulated and PvdS-dependent.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0002049 pyoverdine biosynthetic process | IMP PMID:12686626 Identification and characterization of novel pyoverdine synt... | MODIFY | Summary: PseudoCAP IMP from a screen that mutated candidate pvd genes and measured pyoverdine. The mutant phenotype (less extracellular pyoverdine) reflects loss of export and recycling, and the full text of PMID:19906986 attributes the lower yield to reduced synthesis secondary to the export defect. The pump does no step of the biosynthetic chemistry. Not an IBD seed. Reason: Indirect phenotype annotated as participation in biosynthesis. The protein takes part in pyoverdine transport, so the claim is re-pointed to GO:0015891 siderophore transport (PSEUDOCAP WRONG_TERM, PROBABLE). Proposed replacements: siderophore transmembrane transport Supporting Evidence: PMID:19906986 our preliminary results suggest that the lower PVD levels in their culture supernatants are a result of reduced PVD synthesis rather than of impaired secretion of de novo synthesized PVD PMID:19906986 Therefore, the entire PvdRT-OpmQ system (i.e., the IM ABC transporter PvdT, the periplasmic fusion protein PvdR, and the OM porin OpmQ) appears to be involved in the transport of PVD from the periplasm to the extracellular milieu. |
| GO:0009279 cell outer membrane | IEA GO_REF:0000044 | ACCEPT | Summary: UniProt subcellular location (cell outer membrane, lipid anchor). OpmQ is an OMF-family lipoprotein, the TolC-like outer-membrane component of the pump. Reason: Location where the channel acts. Supporting Evidence: PMID:19906986 PvdRT-OpmQ displays the typical architecture of Gram-negative tripartite ABC-type exporters, consisting of an IM component with both ATPase and permease domains, a periplasmic membrane fusion protein, and a TolC-like OM protein |
| GO:0015562 efflux transmembrane transporter activity | IDA PMID:19906986 Molecular basis of pyoverdine siderophore recycling in Pseud... | ACCEPT | Summary: PseudoCAP row whose descendant term (efflux transmembrane transporter activity is_a transmembrane transporter activity) seeds the PTN008411811 IBD on GO:0022857. Seed verdict SOUND. Full text read: mutant phenotype only, so IDA is the wrong code. Reason: Claim correct; evidence code recorded as a PSEUDOCAP defect. Supporting Evidence: PMID:19906986 Therefore, the entire PvdRT-OpmQ system (i.e., the IM ABC transporter PvdT, the periplasmic fusion protein PvdR, and the OM porin OpmQ) appears to be involved in the transport of PVD from the periplasm to the extracellular milieu. |
| GO:0015562 efflux transmembrane transporter activity | IDA PMID:21035449 An efflux pump is involved in secretion of newly synthesized... | ACCEPT | Summary: PseudoCAP row whose descendant term (efflux transmembrane transporter activity is_a transmembrane transporter activity) seeds the PTN008411811 IBD on GO:0022857. Seed verdict SOUND. Abstract shows export of newly made PVD by the pump. Reason: Supported export function of the pump. Supporting Evidence: PMID:21035449 Bacteria lacking this efflux pump accumulated PVD, or a fluorescent precursor, in the periplasm, due to their inability to efficiently secrete into the media newly synthesized PVD. |
| GO:0015562 efflux transmembrane transporter activity | IDA PMID:22187978 The PvdRT-OpmQ efflux pump controls the metal selectivity of... | ACCEPT | Summary: PseudoCAP row whose descendant term (efflux transmembrane transporter activity is_a transmembrane transporter activity) seeds the PTN008411811 IBD on GO:0022857. Seed verdict SOUND. Reason: Supported export function of the pump. Supporting Evidence: PMID:22187978 PvdRT-OpmQ is an ATP-dependent efflux pump involved in the secretion of newly synthesized pyoverdine (PVD) and of PVD that has transported and released its iron into the bacterium from the periplasm into the extracellular medium. |
| GO:0015562 efflux transmembrane transporter activity | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro OEP mapping. Reason: Consistent with the experimental rows. Supporting Evidence: PMID:19906986 Therefore, the entire PvdRT-OpmQ system (i.e., the IM ABC transporter PvdT, the periplasmic fusion protein PvdR, and the OM porin OpmQ) appears to be involved in the transport of PVD from the periplasm to the extracellular milieu. |
| GO:0015562 efflux transmembrane transporter activity | IMP PMID:19906986 Molecular basis of pyoverdine siderophore recycling in Pseud... | ACCEPT | Summary: PseudoCAP row whose descendant term (efflux transmembrane transporter activity is_a transmembrane transporter activity) seeds the PTN008411811 IBD on GO:0022857. Seed verdict SOUND. opmQ mutant accumulates periplasmic PVD; complemented. Reason: Genetic evidence that the system exports PVD. Supporting Evidence: PMID:19906986 Conversely, PA2389 , PA2390 , and opmQ mutants accumulated five- to sixfold higher amounts of PVD than wild-type PAO1, suggesting an involvement of these genes in PVD export. |
| GO:0015562 efflux transmembrane transporter activity | IMP PMID:22187978 The PvdRT-OpmQ efflux pump controls the metal selectivity of... | ACCEPT | Summary: PseudoCAP row whose descendant term (efflux transmembrane transporter activity is_a transmembrane transporter activity) seeds the PTN008411811 IBD on GO:0022857. Seed verdict SOUND. Reason: Genetic evidence that the system exports PVD-metal complexes. Supporting Evidence: PMID:22187978 the PvdRT-OpmQ efflux pump exports unwanted metals complexed with PVD from the bacterium |
| GO:0015562 efflux transmembrane transporter activity | IMP PMID:23766114 An efflux pump is required for siderophore recycling by Pseu... | ACCEPT | Summary: PseudoCAP row whose descendant term (efflux transmembrane transporter activity is_a transmembrane transporter activity) seeds the PTN008411811 IBD on GO:0022857. Seed verdict SOUND. Reason: Genetic evidence that the system recycles PVD. Supporting Evidence: PMID:23766114 Mutation of genes encoding this efflux pump (named PvdRT-OpmQ) prevented recycling of PVDI from the periplasm into the extracellular medium. |
| GO:0016020 membrane | IBA GO_REF:0000033 | TOO GENERAL | Summary: IBA from PTN008411811 (OMF clade, 85 leaves, 20 taxa). Seeds are OpmQ (via its efflux pump complex rows), OprM (Q51487; cell outer membrane EXP, efflux pump complex IDA) and OprJ (Q51397; outer membrane IDA). Stands without OpmQ. Reason: True, but entailed by GO:0009279 cell outer membrane and GO:1990281 efflux pump complex, both accepted here. The node term is deliberately generic and suits the clade. |
| GO:0016020 membrane | IEA GO_REF:0000002 | TOO GENERAL | Summary: InterPro MdtP/NodT-like mapping. Reason: Entailed by GO:0009279 cell outer membrane, accepted above. |
| GO:0022857 transmembrane transporter activity | IBA GO_REF:0000033 | TOO GENERAL | Summary: IBA from PTN008411811. Seeds OprM (efflux transporter IDA/IMP), OprJ (IMP/IGI), E. coli CusC (P77211; copper transporter IGI) and OpmQ. Stands without OpmQ. Reason: Entailed by GO:0015562 efflux transmembrane transporter activity, accepted above. |
| GO:0022857 transmembrane transporter activity | IEA GO_REF:0000002 | TOO GENERAL | Summary: InterPro mapping. Reason: Entailed by GO:0015562, accepted above. |
| GO:0055085 transmembrane transport | IBA GO_REF:0000033 | MODIFY | Summary: IBA from PTN008411811 seeded by OprJ, OprM and CusC (not by OpmQ). Generic transport, sound at the node. Reason: Correct for OpmQ, and its substrate is known, so GO:0044718 siderophore transmembrane transport is the informative term: its definition is explicitly membrane-crossing and it is the only transmembrane-specific siderophore process term. Note that GO:0044718 is_a GO:0015891 only, and neither is a descendant of GO:0055085 (checked in go-basic.obo and QuickGO, 2026-11-06), so this refinement does not formally retain the transmembrane-transport ancestry; that looks like a missing is_a in GO and is raised as a question below. The node-level claim is not disputed. Propagation Review Root cause: NO FAILURE CORE Failure modes: GRANULARITY MISMATCH Sources checked: PANTHER:PTN008411811 · PTN008411811 SUPPORTS TRANSFER OMF clade; generic transport is the right node-level term. UniProtKB:P77211 · cusC (E. coli) SUPPORTS TRANSFER Experimental copper efflux evidence; a valid seed for generic transport. Proposed replacements: siderophore transmembrane transport Supporting Evidence: PMID:19906986 we identified a tripartite ATP-binding cassette efflux transporter, here named PvdRT-OpmQ, which translocates PVD from the periplasmic space to the extracellular milieu |
| GO:0055085 transmembrane transport | IEA GO_REF:0000002 | MODIFY | Summary: InterPro mapping to generic transmembrane transport. Reason: As for the IBA row; refine to siderophore transport. Proposed replacements: siderophore transmembrane transport Supporting Evidence: PMID:19906986 we identified a tripartite ATP-binding cassette efflux transporter, here named PvdRT-OpmQ, which translocates PVD from the periplasmic space to the extracellular milieu |
| GO:1990281 efflux pump complex | IDA PMID:19906986 Molecular basis of pyoverdine siderophore recycling in Pseud... | ACCEPT | Summary: PseudoCAP row whose term (efflux pump complex, a membrane protein complex) seeds the PTN008411811 IBD on GO:0016020 membrane. Seed verdict SOUND. Full text read: membership inferred from operon, architecture and mutant phenotypes; IDA is the wrong code. Reason: Claim correct; evidence code recorded as a PSEUDOCAP defect. Supporting Evidence: PMID:19906986 PvdRT-OpmQ displays the typical architecture of Gram-negative tripartite ABC-type exporters, consisting of an IM component with both ATPase and permease domains, a periplasmic membrane fusion protein, and a TolC-like OM protein |
| GO:1990281 efflux pump complex | IDA PMID:21035449 An efflux pump is involved in secretion of newly synthesized... | ACCEPT | Summary: PseudoCAP row whose term (efflux pump complex, a membrane protein complex) seeds the PTN008411811 IBD on GO:0016020 membrane. Seed verdict SOUND. Reason: Component of the PvdRT-OpmQ pump. Supporting Evidence: PMID:21035449 Bacteria lacking this efflux pump accumulated PVD, or a fluorescent precursor, in the periplasm, due to their inability to efficiently secrete into the media newly synthesized PVD. |
| GO:1990281 efflux pump complex | IDA PMID:22187978 The PvdRT-OpmQ efflux pump controls the metal selectivity of... | ACCEPT | Summary: PseudoCAP row whose term (efflux pump complex, a membrane protein complex) seeds the PTN008411811 IBD on GO:0016020 membrane. Seed verdict SOUND. Reason: Component of the PvdRT-OpmQ pump. Supporting Evidence: PMID:22187978 PvdRT-OpmQ is an ATP-dependent efflux pump involved in the secretion of newly synthesized pyoverdine (PVD) and of PVD that has transported and released its iron into the bacterium from the periplasm into the extracellular medium. |
| GO:1990281 efflux pump complex | IMP PMID:19906986 Molecular basis of pyoverdine siderophore recycling in Pseud... | ACCEPT | Summary: PseudoCAP row whose term (efflux pump complex, a membrane protein complex) seeds the PTN008411811 IBD on GO:0016020 membrane. Seed verdict SOUND. Reason: Component of the PvdRT-OpmQ pump. Supporting Evidence: PMID:19906986 Therefore, the entire PvdRT-OpmQ system (i.e., the IM ABC transporter PvdT, the periplasmic fusion protein PvdR, and the OM porin OpmQ) appears to be involved in the transport of PVD from the periplasm to the extracellular milieu. |
| GO:1990281 efflux pump complex | IMP PMID:22187978 The PvdRT-OpmQ efflux pump controls the metal selectivity of... | ACCEPT | Summary: PseudoCAP row whose term (efflux pump complex, a membrane protein complex) seeds the PTN008411811 IBD on GO:0016020 membrane. Seed verdict SOUND. Reason: Component of the PvdRT-OpmQ pump. Supporting Evidence: PMID:22187978 the PvdRT-OpmQ efflux pump exports unwanted metals complexed with PVD from the bacterium |
| GO:1990281 efflux pump complex | IMP PMID:23766114 An efflux pump is required for siderophore recycling by Pseu... | ACCEPT | Summary: PseudoCAP row whose term (efflux pump complex, a membrane protein complex) seeds the PTN008411811 IBD on GO:0016020 membrane. Seed verdict SOUND. Reason: Component of the PvdRT-OpmQ pump. Supporting Evidence: PMID:23766114 Mutation of genes encoding this efflux pump (named PvdRT-OpmQ) prevented recycling of PVDI from the periplasm into the extracellular medium. |
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Download this section (compressed HTML)Q: GO:0044718 siderophore transmembrane transport is_a GO:0015891 siderophore transport only, and neither term is a descendant of GO:0055085 transmembrane transport, although the definition of GO:0044718 is explicitly membrane-crossing and sibling terms such as GO:0034219 carbohydrate transmembrane transport do sit under GO:0055085. Should GO:0044718 gain that is_a, so that refining a GO:0055085 row to it keeps the transmembrane claim?
Q: Can OpmQ substitute for, or be substituted by, other OMFs (OprM, OprJ) in pyoverdine export, as OMF promiscuity in other P. aeruginosa pumps would suggest?
Experiment: Test cross-complementation of an opmQ deletion with oprM or oprJ for periplasmic pyoverdine accumulation and recycling.
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