Hsero_1011 notes

2026-11-04 session (Claude, AI-assisted)

• Fetched with just fetch-gene HERSS <accession> --alias Hsero_1011: the gene-name lookup
  failed because the UniProt stream endpoint returned 503, so the accession route was used.
• No provider deep-research file was generated (no provider API keys in this session).
  The review rests on the UniProt record, the cached pathway papers
  PMID:27059806 (abstract only) and, for fdeE, PMID:39107441 (full text), the
  KEGG queries in genes/HERSS/Hsero_1007/Hsero_1007-bioinformatics/, and the P.
  putida ortholog reviews (PSEPK PP_3195-PP_3206) with their committed alignments.
• Literature search (PubMed E-utilities, 2026-11-04): "naringenin Herbaspirillum"
  (13 hits), "fdeE naringenin" (2: PMID:27059806, PMID:39107441), "Hsero_1007"
  (1: PMID:27059806). Pathway-relevant hits cached: PMID:23125118 (fde operon induced
  by naringenin; fdeA and fdeR mutants cannot degrade naringenin), PMID:27059806
  (fdeE, fdeC, fdeG mutants), PMID:27878922 (FdeR activator), PMID:39107441 (purified
  FdeE). Only FdeE has been assayed biochemically; only fdeA, fdeC, fdeE, fdeG and fdeR
  have been mutated.
• Context: written for the module modules/bacterial_flavonoid_degradation.yaml.

2026-11-06 — comparative fde audit

Read the 2013 full paper through its author-uploaded copy; its fdeA mutation is probably polar. Preserve the distinction between locus-level inference and exact catalytic assignment. See modules/bacterial_flavonoid_degradation-notes.md for source access and comparative boundaries.

2026-11-06 — late-component participation reassessment

The inherited GO:0046275 proposal is withdrawn and explicitly retired: true: the FAH fold supports multiple reaction classes, while the proposed R13078/R13079 transformations are untested. Locus induction, whole-operon phenotypes and similarity to another unassayed candidate do not establish this product's individual step. Original source fields and row position are preserved; retirement records curator withdrawal, not an upstream GOA disappearance. The former process-only core block is removed, and the unresolved role remains a knowledge gap. The same-role BRADU comparator bll6422 likewise asserts no process annotation. See analysis/module_audits/bacterial_flavonoid_degradation/round1-source-review.md.

2026-11-07 PR #6140 round-2 review follow-up

The inherited GO:0046275 proposal now uses REMOVE with its existing retired:true flag. This explicitly withdraws a curator-authored proposal, following the documented cysI precedent, rather than making a biological absence claim or reporting disappearance from upstream GOA. Original payload, position and evidence remain present.

See analysis/module_audits/bacterial_flavonoid_degradation/round2-review-response.md for source provenance, limits and disposition of all seven review points. Earlier journal entries record superseded judgments and remain unchanged.