PP_3204 encodes a cupin type-2 domain protein in the KT2440 flavonoid-degradation locus. KEGG assigns it to FdeH orthology group K26182, one of two proteins associated with the predicted R13075 dioxygenation and A-ring-cleavage step. Its contribution to that reaction is unresolved, so no molecular-function term is assigned independently of the FdeC catalyst.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0046275 flavonoid catabolic process | ISS file:PSEPK/PP_3204/PP_3204-bioinformatics/RESULTS.md | REMOVE | Summary: Withdraw the inherited FdeH process proposal; an individual flavonoid-catabolic step has not been established. Reason: The conserved locus and orthology identify a candidate FdeH protein, but cupin membership and similarity to unassayed Hsero_1010 do not establish a particular catalytic or accessory contribution. The available whole-operon phenotype, including the probably polar fdeA insertion, does not show which step this individual protein performs. There is no independently assayed donor for this particular role; the corresponding BRADU comparator bll6423 likewise carries no process assertion. Retain the original source payload and row position while withdrawing the active proposal. The retired flag records this curator decision, not disappearance of an upstream GOA row or proof of biological absence. Native participation remains an open question. REMOVE records withdrawal of this earlier curator-authored NEW proposal, not removal of a current GOA assertion. It does not claim that the protein is biologically incapable of participating in flavonoid catabolism. Supporting Evidence: file:PSEPK/PP_3204/PP_3204-bioinformatics/RESULTS.md KEGG target mapping: `ppu:PP_3204 -> ko:K26182` file:PSEPK/PP_3204/PP_3204-bioinformatics/RESULTS.md Pairwise identity over aligned residue pairs: 57.6% |
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Download this section (compressed HTML)Q: Is PP_3204 catalytic, metal-binding, or an accessory factor for PP_3197 during R13075?
Experiment: Reconstitute PP_3197 with and without PP_3204 using the R13075 substrate, measuring turnover, metal dependence, complex formation, and product identity.
Type: biochemical reconstitution and interaction analysis
What is not known — curated, literature-grounded statements of the open unknowns (the inverse of core functions).
Gap: FdeH's biochemical contribution to the shared R13075 step is unknown.
OPEN BIOLOGYCURATION
What is known: FdeH membership and pathway placement nominate a candidate; they do not establish which native flavonoid-catabolic step the target performs. The inherited process proposal is retired pending participation evidence.
Significance: A molecular-function annotation would be speculative until FdeH is tested independently and with FdeC.
What would resolve it: Compare R13075 turnover by purified FdeC alone and with FdeH, and test metal binding and catalytic-residue substitutions in FdeH.
Provenance (the field's own admissions):
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