ARBA00095398 ribophagy (GO:0034517)

id: ARBA00095398
description: >-
  Assigns GO:0034517 (ribophagy) to Saccharomycotina proteins that match both 60S ribosomal protein L12
  (uL11) CATH FunFams, 1.10.10.250:FF:000002 and 3.30.1550.10:FF:000002.
status: COMPLETE
rule_type: ARBA
rule:
  rule_id: ARBA00095398
  condition_sets:
  - number: 1
    conditions:
    - condition_type: FUNFAM
      value: 1.10.10.250:FF:000002
      curie: CATH.FunFam:1.10.10.250:FF:000002
      label: 60S ribosomal protein L12
      negated: false
    - condition_type: FUNFAM
      value: 3.30.1550.10:FF:000002
      curie: CATH.FunFam:3.30.1550.10:FF:000002
      label: 60S ribosomal protein L12
      negated: false
    - condition_type: TAXON
      value: Saccharomycotina
      curie: NCBITaxon:147537
      label: Saccharomycotina
      negated: false
    notes: >-
      Swiss-Prot entries matching the whole conjunction: 3 (UniProtKB query, 2026-11-10); unreviewed entries:
      159. Swiss-Prot matches: P0CX54 (RPL12B), P0CX53 (RPL12A), Q5AJF7 (RPL12). Experimental annotation
      to GO:0034517 ribophagy or an is_a/part_of descendant (QuickGO): P0CX53 RPL12A GO:0034517 ribophagy
      IGI PMID:39934334 (SGD); P0CX54 RPL12B GO:0034517 ribophagy IGI PMID:39934334 (SGD).
  go_annotations:
  - go_id: GO:0034517
    go_label: ribophagy
    aspect: BP
  entries: []
  reviewed_protein_count: 0
  unreviewed_protein_count: 0
  created_date: '2025-12-15'
  modified_date: '2026-07-18'
  source_condition_set_count: 1
  retrieved_date: '2026-11-09'
review_summary: >-
  The rule has one condition set and it was examined. Its Swiss-Prot matches are S. cerevisiae RPL12A
  (P0CX53) and RPL12B (P0CX54) and C. albicans RPL12 (Q5AJF7). SGD annotates both S. cerevisiae proteins
  to ribophagy by IGI from PMID:39934334, "Rpl12 is a conserved ribophagy receptor", with the qualifier
  acts_upstream_of_or_within. The C. albicans protein has no curated ribophagy annotation, and the 159
  unreviewed matches across Saccharomycotina rest on transfer from the two S. cerevisiae paralogs.
action: ACCEPT
action_rationale: >-
  The only condition set identifies uL11 in budding yeasts, and the two reviewed S. cerevisiae members
  carry an experimental annotation to the exact term. Confidence is moderate because the support is a
  single paper and one species, and the curated qualifier is acts_upstream_of_or_within rather than involved_in.
literature_support:
  assessment: MODERATE
  notes: >-
    One primary paper, PMID:39934334 (Nat Cell Biol 2025), is the source of the SGD IGI annotations of
    P0CX53 and P0CX54 to GO:0034517. The paper is not in the local publication cache, so no quotation
    is given.
annotation_assessments:
- annotation_kind: GO_TERM
  value: GO:0034517
  label: ribophagy
  assessment: CORRECT
  correct_examples:
  - P0CX53
  - P0CX54
  notes: >-
    P0CX53 RPL12A GO:0034517 IGI PMID:39934334 (SGD, acts_upstream_of_or_within); P0CX54 RPL12B GO:0034517
    IGI PMID:39934334 (SGD, acts_upstream_of_or_within). Q5AJF7 (C. albicans RPL12) also matches the set
    and has no curated annotation to the term.
confidence: 0.6
references:
- id: PMID:39934334
  title: Rpl12 is a conserved ribophagy receptor.
corrections:
- date: '2026-11-10'
  withdrawn_claim: >-
    Ribosomal structural proteins cannot mediate ribosome degradation, and no literature supports a role
    of L12 proteins in autophagy.
  correction: >-
    S. cerevisiae RPL12A and RPL12B are curated to ribophagy from an experimental paper that describes
    Rpl12 as a ribophagy receptor.
  error_type: REFUTED_BY_CURATED_ANNOTATION
  evidence:
  - UniProtKB:P0CX53 GO:0034517 IGI PMID:39934334 (SGD)
  - UniProtKB:P0CX54 GO:0034517 IGI PMID:39934334 (SGD)
  - 'PMID:39934334 title (Europe PMC): Rpl12 is a conserved ribophagy receptor.'
- date: '2026-11-10'
  withdrawn_claim: The rule no longer exists in the UniProt ARBA system.
  correction: The rule is live.
  error_type: UNEXAMINED_RULE
  evidence:
  - >-
    https://rest.uniprot.org/arba/ARBA00095398 returned HTTP 200 on 2026-11-09 with one condition set
    and modifiedDate 2026-07-18
- date: '2026-11-10'
  withdrawn_claim: The rule annotates S. pombe rpl1201/rpl1202.
  correction: The live condition set is restricted to Saccharomycotina, which does not contain S. pombe.
  error_type: STALE_RULE_VERSION
  evidence:
  - >-
    Live condition set 1: FunFam 1.10.10.250:FF:000002 AND FunFam 3.30.1550.10:FF:000002 AND taxon Saccharomycotina
    (NCBITaxon:147537)
  - 'Swiss-Prot matches of the full conjunction: P0CX53, P0CX54, Q5AJF7'
- date: '2026-11-10'
  withdrawn_claim: Every assessment was supported by the rule's own deep-research note.
  correction: >-
    That note is not an independent source; the assessment blocks that rested on it were removed.
  error_type: UNSUPPORTED_SOURCE
  evidence:
  - >-
    All supported_by entries of the previous version cited rules/arba/ARBA00095398/ARBA00095398-deep-research-manual.md