Reviewed RidA-ai-review.yaml against all 22 physical rows in RidA-goa.tsv,
the cached UniProt record, all seven cached PMID records cited by experimental
annotations, the Falcon deep-research summary, the unfolded-protein-binding
project policy, and current PTHR11803 PAINT data. The public qualifier-backfill
wrapper restored the exact GOA qualifiers before review. Coverage is 22/22 with
no duplicate or missing physical signature: 10 enables, 4 involved_in, 4
located_in, 2 acts_upstream_of_or_within, 1 is_active_in, and 1 part_of.
RidA's core function is the cytosolic hydrolysis of reactive enamine/imine
intermediates generated by PLP-dependent enzymes. The family study states that
YjgF proteins "have enamine/imine deaminase activity and accelerate the release
of ammonia from reactive enamine/imine intermediates" generated by IlvA
PMID:22094463. The E. coli redox-proteomics paper independently calls RidA an
"enamine/imine deaminase" and reports direct in-vitro activity regulation
PMID:23696645. The broad hydrolase and amino-acid-biosynthesis mappings were
therefore narrowed to GO:0120241 and GO:0009082. The current GOA export itself
labels GO:0009097 obsolete, so its valid pathway meaning was redirected to the
verified current replacement GO:1901705 (L-isoleucine biosynthetic process),
preserving branch specificity rather than duplicating the broad GO:0009082 row.
The 1.2 Å structure reports, verbatim, "The YjgF molecule is a homotrimer with
exact threefold symmetry" PMID:10595546. Homotrimerization and complex
membership remain core structural annotations; generic identical protein
binding is retained as non-core because it adds no mechanistic information.
PMID:25517874 provides full-text, direct evidence that HOCl- or chloramine-treated
RidA is an ATP-independent holdase. It reports that "The addition of ATP did not
enhance chaperone activity, consistent with a holdase function of HOCl-treated
RidA" and that untreated RidA had no effect on IlvA aggregation. Thus the biology
is real but explicitly modification-dependent. The GO:0051082 IDA row is changed
to MODIFY toward the established NTR for general "holdase chaperone activity."
GO:0140309 is not suitable because the experiments demonstrate in-situ aggregation
prevention, not escort to a defined acceptor molecule or location. GO:0051082 is
formally obsolete, as recorded in projects/UNFOLDED_PROTEIN_BINDING.md and
go-ontology#30962. A top-level proposed term records the project definition and
the exact RidA evidence.
The two response-to-toxic-substance annotations remain valid but non-core:
PMID:25517874 directly states "Deletion of ridA results in an HOCl-sensitive
phenotype." This is a conditional stress role rather than the constitutive
deaminase function.
Both IBA rows trace to PANTHER:PTN000211014 in PTHR11803. The cached current
PAINT file interpro/panther/PTHR11803/PTHR11803-paint.tsv retains GO:0005829
(dated 2024-07-29) and GO:0019239 (dated 2026-05-28) at that node. Exact
qualifier-aware GOA WITH/FROM entities were copied into supporting_entities.
RidA itself appears among the descendant evidence for both assertions; per
projects/IBA_REVIEW.md, this is expected experimental grounding and is not
circular. Both propagations are classified NO_FAILURE_CORE.
PMID:16858726 is abstract-only in the repository cache. A primary-source search
located a publisher supporting-information row for yjgF under legacy accession
P39330, which the cached UniProt record verifies as a secondary accession of
RidA P0AF93. This confirms provenance but does not distinguish genuine membrane
association from fractionation carryover. The membrane HDA is therefore retained
as KEEP_AS_NON_CORE out of deference to the high-throughput experimental
annotation, while independent cytosol annotations and the soluble structure
establish cytosol as the primary location. The PMID is marked full-text-unavailable
and its manual correctness assessment remains UNVERIFIED. PMID:15911532 is also
abstract-only; its broad fractionation description is compatible with the cytosol
IDA, so that experimental annotation is retained with curator deference.
Final action distribution: 13 ACCEPT, 4 KEEP_AS_NON_CORE, 5 MODIFY, 0 UNDECIDED,
0 REMOVE, 0 MARK_AS_OVER_ANNOTATED, and 0 PENDING. With every physical signature
resolved, the overall review is COMPLETE.