ARBA00023002

id: ARBA00023002
description: Assigns the UniProt keyword KW-0560 Oxidoreductase through 2158 alternative condition sets
  of InterPro, PANTHER and CATH FunFam signatures, some with a taxon condition.
status: IN_PROGRESS
rule_type: ARBA
rule:
  rule_id: ARBA00023002
  condition_sets:
  - number: 2
    conditions:
    - condition_type: INTERPRO
      value: IPR036291
      curie: InterPro:IPR036291
      label: NAD(P)-binding domain superfamily
      interpro_type: HOMOLOGOUS_SUPERFAMILY
      negated: false
    - condition_type: INTERPRO
      value: IPR046346
      curie: InterPro:IPR046346
      label: Aminoacid dehydrogenase-like, N-terminal domain superfamily
      interpro_type: HOMOLOGOUS_SUPERFAMILY
      negated: false
    - condition_type: TAXON
      value: '3379134'
      curie: NCBITaxon:3379134
      label: Pseudomonadati
      negated: false
    notes: 'UniProtKB query, November 2026: 951 Swiss-Prot and 57658 TrEMBL entries match; 951 of the
      951 Swiss-Prot entries carry keyword KW-0560 Oxidoreductase.'
  - number: 4
    conditions:
    - condition_type: INTERPRO
      value: IPR008927
      curie: InterPro:IPR008927
      label: 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily
      interpro_type: HOMOLOGOUS_SUPERFAMILY
      negated: false
    - condition_type: TAXON
      value: '1236'
      curie: NCBITaxon:1236
      label: Gammaproteobacteria
      negated: false
    notes: 'UniProtKB query, November 2026: 743 Swiss-Prot and 42514 TrEMBL entries match; 743 of the
      743 Swiss-Prot entries carry keyword KW-0560 Oxidoreductase.'
  - number: 456
    conditions:
    - condition_type: INTERPRO
      value: IPR001424
      curie: InterPro:IPR001424
      label: Superoxide dismutase, copper/zinc binding domain
      interpro_type: DOMAIN
      negated: false
    - condition_type: INTERPRO
      value: IPR018152
      curie: InterPro:IPR018152
      label: Superoxide dismutase, copper/zinc, binding site
      interpro_type: BINDING_SITE
      negated: false
    - condition_type: TAXON
      value: '71275'
      curie: NCBITaxon:71275
      label: rosids
      negated: false
    notes: 'UniProtKB query, November 2026: 13 Swiss-Prot and 1091 TrEMBL entries match; 13 of the 13
      Swiss-Prot entries carry keyword KW-0560 Oxidoreductase.'
  - number: 521
    conditions:
    - condition_type: INTERPRO
      value: IPR024134
      curie: InterPro:IPR024134
      label: Superoxide dismutase (Cu/Zn)/superoxide dismutase copper chaperone
      interpro_type: FAMILY
      negated: false
    - condition_type: INTERPRO
      value: IPR036423
      curie: InterPro:IPR036423
      label: Superoxide dismutase-like, copper/zinc binding domain superfamily
      interpro_type: HOMOLOGOUS_SUPERFAMILY
      negated: false
    - condition_type: TAXON
      value: '6231'
      curie: NCBITaxon:6231
      label: Nematoda
      negated: false
    notes: 'UniProtKB query, November 2026: 10 Swiss-Prot and 536 TrEMBL entries match; 10 of the 10 Swiss-Prot
      entries carry keyword KW-0560 Oxidoreductase.'
  entries: []
  reviewed_protein_count: 0
  unreviewed_protein_count: 7183973
  created_date: '2020-05-12'
  modified_date: '2026-07-18'
  retrieved_date: '2026-11-09'
  source_condition_set_count: 2158
review_summary: 'Four of the 2158 live condition sets were examined (sets 2, 4, 456 and 521); the rest
  were not read. In each examined set every matching Swiss-Prot entry carries the Oxidoreductase keyword
  (951 of 951, 743 of 743, 13 of 13 and 10 of 10). An earlier report of the keyword on copper chaperone
  for superoxide dismutase (Drosophila Ccs, E1JH26) could not be reproduced: the entry is now in Swiss-Prot
  without the keyword, and no live condition set matches its signatures and taxon.'
action: UNDECIDED
action_rationale: The rule was sampled, not examined set by set, and no wrongly annotated protein was
  confirmed. The four sets that were checked are supported.
annotation_assessments:
- annotation_kind: KEYWORD
  value: KW-0560
  label: Oxidoreductase
  assessment: UNDECIDED
  notes: 'Sets 2, 4, 456 and 521: all Swiss-Prot matches carry the keyword (counts in rule.condition_sets[].notes).
    The other 2154 sets were not examined.'
corrections:
- date: '2026-11-10'
  withdrawn_claim: IPR008927 is 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase, a kinase/phosphatase,
    and is a clear false positive to remove immediately.
  correction: IPR008927 is the dehydrogenase superfamily "6-phosphogluconate dehydrogenase-like, C-terminal
    domain superfamily". In the rule it occurs only together with Gammaproteobacteria (set 4), where all
    Swiss-Prot matches are oxidoreductases by keyword.
  error_type: WRONG_IDENTIFIER_MEANING
  evidence:
  - 'InterPro API: IPR008927 name "6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily",
    type homologous_superfamily'
  - 'UniProtKB query (xref:interpro-IPR008927) AND (taxonomy_id:1236) AND (reviewed:true): 743 entries;
    with (keyword:KW-0560): 743'
- date: '2026-11-10'
  withdrawn_claim: IPR036291 (NAD(P)-binding domain) occurs in kinases, transferases and hydrolases, so
    the rule needs extra constraints on it.
  correction: IPR036291 never stands alone in the rule. Its only set also requires IPR046346 (Aminoacid
    dehydrogenase-like, N-terminal domain superfamily) and Pseudomonadati, and all Swiss-Prot matches
    of that set are oxidoreductases by keyword.
  error_type: CONJUNCTION_IGNORED
  evidence:
  - 'Live rule set 2: IPR036291 AND IPR046346 AND Pseudomonadati (rest.uniprot.org/arba/ARBA00023002,
    2026-11-09)'
  - 'UniProtKB query for set 2 with reviewed:true: 951 entries; with (keyword:KW-0560): 951'
- date: '2026-11-10'
  withdrawn_claim: GitHub issues document systematic false positives on CCS copper chaperones (E1JH26,
    O14618), caused by overly broad structural domains.
  correction: Two proteins do not establish a rate, and the cause was a guess. On the live data the Drosophila
    entry no longer has the keyword and no live set matches it.
  error_type: SAMPLE_OVERGENERALISED
  evidence:
  - 'UniProtKB E1JH26 (CCS_DROME, reviewed): KW line has no Oxidoreductase (retrieved 2026-11-10)'
  - 'Live sets containing its InterPro signatures: set 456 (IPR001424 AND IPR018152 AND rosids) and set
    521 (IPR024134 AND IPR036423 AND Nematoda); neither taxon includes Drosophila'
  - No live set uses its FunFam 2.60.40.200:FF:000004 or PANTHER PTHR10003
- date: '2026-11-10'
  withdrawn_claim: 2105 condition sets exceed reasonable limits, so the rule must be modified and partitioned.
  correction: The number of alternative sets is not evidence that any of them is wrong.
  error_type: SIZE_AS_EVIDENCE
  evidence:
  - 'src/ai_gene_review/etl/rule_analysis.py: max_condition_sets: int = 12 (default of the overlap-analysis
    tool)'
- date: '2026-11-10'
  withdrawn_claim: GO specificity is mismatched because the rule gives a keyword and no GO term.
  correction: Assigning a keyword is what this rule is for; the absence of a GO consequent is not an error
    in it.
  error_type: OTHER
  evidence:
  - 'rest.uniprot.org/arba/ARBA00023002 annotations: keyword KW-0560 Oxidoreductase only'