Alkyl Hydroperoxide Reductase Activity — Obsoletion & Replacement

IN_PROGRESS OBSOLETION

Alkyl Hydroperoxide Reductase Activity — Obsoletion & Replacement

Overview

A GO obsoletion has retired one molecular function term and merged its
annotations into a broader, more accurate term:

Replaced by:

The rationale, captured in the upstream go-ontology ticket, is that
GO:0008785 was defined with a substrate-specific stoichiometry
(octane hydroperoxide + NADH + H+ = H2O + NAD+ + 1-octanol) that is
more specific than the specificity of any known gene product, and
"alkyl hydroperoxide reductase" is listed by Expasy as a synonym of
EC 1.11.1.26 — i.e. exactly the broader term GO:0102039.

This project tracks the impact on AI Gene Review and queues the
affected genes for review. Neither gene is currently in this
repository.

Upstream tickets

Obsoletion plan (per upstream)

Obsoleted term ID Replacement
alkyl hydroperoxide reductase activity GO:0008785 (obsolete) GO:0102039 NADH-dependent peroxiredoxin activity

Affected experimental annotations (from upstream issue body)

Only 2 direct experimental annotations remain on the books; both
need to be moved from GO:0008785 to GO:0102039.

Group Gene Species Source ID Reference Evidence PANTHER Status
EcoliWiki AhpF E. coli K-12 (NCBITaxon:83333) EcoCyc:EG11385-MONOMER PMID:11717276 IGI (with ahpC, katE, katG) — pending move to GO:0102039
PseudoCAP PA3529 P. aeruginosa PAO1 (NCBITaxon:208964) UniProtKB:Q9HY81 PMID:21674802 IDA PTHR10681 pending move to GO:0102039

No InterPro2GO, UniProt-Keywords, or UniRule mappings to GO:0008785
were listed in the upstream issue.

Impact on this repo

No genes annotated to GO:0008785 are currently reviewed here.
Searches under genes/ECOLI/ and genes/PSEAE/ for AhpF / PA3529
returned no matches.

So no existing reviews need refresh for the obsoletion itself,
but two prokaryotic redox-enzyme reviews are now natural follow-on
work since the obsoletion is in production and the annotation
migration is the only remaining loose end upstream.

The PANTHER family PTHR10681 (alkyl hydroperoxide reductase
subunit F / thioredoxin reductase-like) appears in the with/from
column for the PA3529 IDA annotation. Any IBA propagation from this
family will also need to be reviewed once GOA pipelines pick up the
obsoletion, but per the upstream issue no IBA migrations are listed
as separate items, so this is opportunistic rather than required.

Scope

Candidate genes for initial review

Verify each with just fetch-gene <organism> <gene> before starting
and confirm UniProt accessions. Neither is currently in the repo.

Tier 1 — direct annotation, well-characterized

  1. AhpF (E. coli K-12, EcoCyc:EG11385-MONOMER) — the FAD-containing
    NADH-dependent disulfide reductase subunit of the AhpC/AhpF system.
    Reduces oxidized AhpC (the peroxiredoxin subunit) at the expense
    of NADH. The IGI annotation from PMID:11717276 was made together
    with ahpC, katE, and katG, so the biological context (peroxide
    detoxification in concert with catalases) is well-defined. A clean
    ACCEPT/MODIFY review target for the obsoletion migration.

Tier 2 — direct annotation, less canonical

  1. PA3529 / Q9HY81 (P. aeruginosa PAO1) — IDA annotation from
    PMID:21674802 by PseudoCAP. PANTHER family PTHR10681 places it in
    the AhpF-like family. Verify gene symbol (PseudoCAP uses locus
    tag) and whether UniProt has a recommended gene name before
    creating the review folder. Slightly lower priority than AhpF
    only because the E. coli enzyme is the textbook reference for the
    activity.

Proposed approach

  1. Obsoletion has landed. GO:0008785 is already obsolete in the
    ontology (PR #32015 merged). The 2 direct annotations in the
    upstream tracker have not yet been migrated as of project
    creation date — that is the open work upstream issue #6396 is
    tracking.
  2. Start with E. coli AhpF. Run just fetch-gene ECOLI AhpF
    (or whichever capitalization UniProt prefers) and confirm the
    GOA pull picks up the obsoletion: GO:0008785 should appear as an
    obsolete term (with replaced_by annotation) and any new IBA pulls
    should already use GO:0102039. Review per CLAUDE.md.
  3. Follow with P. aeruginosa PA3529 (Q9HY81). The gene symbol
    may differ between UniProt and PseudoCAP — verify before
    creating the folder.
  4. Cross-reference GO:0009321 (alkyl hydroperoxide reductase
    complex, CC) — this term is intact and is the appropriate CC for
    the AhpC/AhpF holocomplex. If reviewing the cognate AhpC
    subunit becomes relevant downstream, it can be added as a Tier 3
    later but is not in scope here (no direct annotation to the
    obsoleted MF).
  5. Defer IBA-propagation review for PTHR10681 until the next GOA
    release reflects the obsoletion; the upstream issue lists no IBA
    migration as required, so this is opportunistic.

Priority

Low. Only 2 direct annotations are affected and the ontology
change is already in production. The opportunity here is that AhpF
and PA3529 are otherwise unreviewed prokaryotic redox enzymes that
would extend the repo's bacterial coverage, not that any existing
review is blocked.

Status