ARBA00029057 protein-containing complex assembly (GO:0065003)

id: ARBA00029057
description: >-
  ARBA rule assigning GO:0065003 protein-containing complex assembly through 88 alternative condition
  sets built from InterPro, CATH FunFam, PANTHER and taxon conditions.
status: IN_PROGRESS
rule_type: ARBA
rule:
  rule_id: ARBA00029057
  condition_sets:
  - number: 4
    conditions:
    - condition_type: INTERPRO
      value: IPR007259
      curie: InterPro:IPR007259
      label: Gamma-tubulin complex component protein
      negated: false
    - condition_type: TAXON
      value: Fungi
      label: Fungi
      negated: false
    notes: Gamma-tubulin complex component protein family, Fungi.
  - number: 5
    conditions:
    - condition_type: INTERPRO
      value: IPR029440
      curie: InterPro:IPR029440
      label: Dynein regulatory complex protein 1, C-terminal
      negated: false
    - condition_type: INTERPRO
      value: IPR039505
      curie: InterPro:IPR039505
      label: Dynein regulatory complex protein 1/2, N-terminal
      negated: false
    - condition_type: INTERPRO
      value: IPR039750
      curie: InterPro:IPR039750
      label: Dynein regulatory complex protein
      negated: false
    notes: Dynein regulatory complex protein signatures.
  - number: 6
    conditions:
    - condition_type: INTERPRO
      value: IPR037494
      curie: InterPro:IPR037494
      label: Rubisco accumulation factor 1
      negated: false
    - condition_type: INTERPRO
      value: IPR040781
      curie: InterPro:IPR040781
      label: Rubisco accumulation factor 1, helix turn helix domain
      negated: false
    - condition_type: INTERPRO
      value: IPR040858
      curie: InterPro:IPR040858
      label: Rubisco accumulation factor 1, C-terminal
      negated: false
    notes: Rubisco accumulation factor 1 family with two of its domains.
  go_annotations:
  - go_id: GO:0065003
    go_label: protein-containing complex assembly
    aspect: BP
  entries: []
  reviewed_protein_count: 0
  unreviewed_protein_count: 0
  created_date: '2021-10-20'
  modified_date: '2026-07-18'
  retrieved_date: '2026-11-09'
  source_condition_set_count: 88
review_summary: >-
  The live rule has 88 condition sets. Three (sets 4, 5 and 6) were read for the identity of their
  InterPro families: gamma-tubulin complex component proteins, dynein regulatory complex proteins
  and Rubisco accumulation factor 1. None was checked against annotated proteins, and 85 sets were
  not examined. No false positive has been identified. No verdict is given.
action: UNDECIDED
action_rationale: The rule was not examined set by set, and nothing verified shows a wrong annotation.
suggested_modifications:
- Examine the condition sets against curated annotations of their Swiss-Prot members.
annotation_assessments:
- annotation_kind: GO_TERM
  value: GO:0065003
  label: protein-containing complex assembly
  assessment: UNDECIDED
  notes: >-
    InterPro API names of the families in sets 4-6: IPR007259 Gamma-tubulin complex component protein;
    IPR029440 Dynein regulatory complex protein 1, C-terminal; IPR039750 Dynein regulatory complex
    protein; IPR037494 Rubisco accumulation factor 1. No matched protein was checked.
corrections:
- date: '2026-11-10'
  withdrawn_claim: >-
    The 89 condition sets span metabolic enzymes, structural proteins, kinases and transport proteins
    with no assembly function.
  correction: >-
    No condition set was recorded and none was named. The sets read since then name complex components
    and an assembly factor.
  error_type: UNEXAMINED_RULE
  evidence:
  - 'Previous file recorded condition_sets: []'
  - 'InterPro API: IPR007259 = Gamma-tubulin complex component protein'
  - 'InterPro API: IPR037494 = Rubisco accumulation factor 1'
- date: '2026-11-10'
  withdrawn_claim: More specific terms such as GO:0006457 protein folding should be used.
  correction: >-
    Protein folding is not a descendant of GO:0065003, so it is not a more specific form of the rule's
    term.
  error_type: ONTOLOGY_MISREAD
  evidence:
  - 'QuickGO is_a ancestors of GO:0006457: GO:0009987, GO:0008150 only'
- date: '2026-11-10'
  withdrawn_claim: GO:0065003 is too broad for meaningful annotation, so the rule should be deprecated.
  correction: A general term that is true of the matched proteins is not an error.
  error_type: GENERAL_IS_NOT_WRONG
  evidence:
  - No wrongly annotated protein was named
- date: '2026-11-10'
  withdrawn_claim: Condition overlap is complete.
  correction: >-
    The same block said overlap analysis was impossible and that no overlap was expected; the assessment
    is removed.
  error_type: OTHER
  evidence:
  - 'Previous condition_overlap notes: "Analysis impossible ... no expected overlap"'
- date: '2026-11-10'
  withdrawn_claim: Literature does not support the rule.
  correction: The only source was the review's own notes file; the assessment is removed.
  error_type: UNSUPPORTED_SOURCE
  evidence:
  - Previous literature_support cited ARBA00029057-deep-research-manual.md only