OprF is the major OmpA/OprF-family outer membrane protein of Pseudomonas putida KT2440. The protein has a signal peptide, an N-terminal outer-membrane beta-barrel porin region, and a C-terminal OmpA-like periplasmic domain. Combined evidence from KT2440 studies and canonical OprF literature supports a core role in outer membrane permeability and envelope integrity, while the current InterPro-derived calcium-binding prediction lacks direct biochemical support.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005509 calcium ion binding | IEA GO_REF:0000002 | REMOVE | Summary: This InterPro-derived annotation is weak for OprF. The established biology of OprF in KT2440 and canonical homologs is outer-membrane localization, porin activity, and envelope integrity rather than calcium binding. Reason: I found no direct biochemical evidence that KT2440 OprF binds calcium. The annotation appears to come from a low-specificity domain match in the acidic C-terminal region and does not reflect the conserved core function of the OprF family. Supporting Evidence: file:PSEPK/oprF/oprF-deep-research-falcon.md The InterPro-derived calcium ion binding annotation is weak: I found no direct biochemical evidence that KT2440 OprF binds calcium, and the predicted thrombospondin type 3 repeat appears non-core relative to the conserved porin/OmpA architecture. |
| GO:0009279 cell outer membrane | IEA GO_REF:0000120 | ACCEPT | Summary: This is the correct specific localization for OprF. Both UniProt and KT2440 literature identify OprF as the major outer membrane porin. Reason: Cell outer membrane localization is directly consistent with the protein architecture, UniProt subcellular annotation, and KT2440 studies manipulating OprF as a major outer membrane porin. Supporting Evidence: PMID:32211393 Then the major outer membrane porin OprF and the specific porin OprE were overproduced during PHA producing conditions on decanoate-grown cells. file:PSEPK/oprF/oprF-deep-research-falcon.md The current evidence supports outer-membrane localization and porin activity as core features of KT2440 OprF. |
| GO:0016020 membrane | IEA GO_REF:0000120 | KEEP AS NON CORE | Summary: This annotation is broadly correct but less informative than the coexisting cell outer membrane annotation. Reason: OprF is certainly a membrane protein, but the more specific and biologically useful localization is GO:0009279 cell outer membrane. Supporting Evidence: file:PSEPK/oprF/oprF-deep-research-falcon.md The current evidence supports outer-membrane localization and porin activity as core features of KT2440 OprF. |
| GO:0015288 porin activity | TAS | NEW | Summary: OprF should carry a core porin activity annotation even though it is absent from the current QuickGO snapshot. KT2440 papers call it the major outer membrane porin, and canonical OprF homologs have direct channel-forming evidence. Reason: This term captures the core molecular function of the OprF family more precisely than broad membrane localization terms. The addition is conservative because it is supported by direct author statements in KT2440 and by classic OprF pore-formation work in the canonical homolog. Supporting Evidence: PMID:32211393 Then the major outer membrane porin OprF and the specific porin OprE were overproduced during PHA producing conditions on decanoate-grown cells. PMID:16595653 The major nonspecific porin of Pseudomonas aeruginosa, OprF, produces a large channel yet allows only a slow diffusion of various solutes. file:PSEPK/oprF/oprF-deep-research-falcon.md Canonical OprF homologs are nonspecific porins; in P. aeruginosa, purified OprF produces large channels, although only a minority of molecules adopt the open pore conformation. |
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Download this section (compressed HTML)Q: Does KT2440 OprF adopt the same low-abundance open-channel conformation described for the canonical Pseudomonas aeruginosa homolog?
Q: Is the InterPro-derived calcium ion binding assignment a false positive, or does the acidic C-terminal region bind calcium under any physiological condition?
Q: How much of the KT2440 ΞoprF envelope phenotype reflects loss of pore function versus loss of OmpA-like periplasmic tethering?
Experiment: Reconstitute purified KT2440 OprF into liposomes or planar bilayers and quantify conductance, selectivity, and open-state frequency.
Type: electrophysiology
Experiment: Complement a KT2440 ΞoprF strain with domain truncations or targeted C-terminal mutants and measure membrane permeability and vesicle production.
Type: genetics
Experiment: Test direct calcium binding of purified full-length OprF or the isolated C-terminal domain by ITC, DSF, or metal-overlay assays.
Type: biochemistry
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