ARBA00022801

id: ARBA00022801
description: >-
  ARBA rule assigning the UniProt keyword Hydrolase (KW-0378) through 4171 alternative condition sets
  built from InterPro, PANTHER and taxon conditions.
status: IN_PROGRESS
rule_type: ARBA
rule:
  rule_id: ARBA00022801
  condition_sets:
  - number: 1
    conditions:
    - condition_type: INTERPRO
      value: IPR014014
      curie: InterPro:IPR014014
      label: RNA helicase, DEAD-box type, Q motif
      negated: false
    - condition_type: INTERPRO
      value: IPR027417
      curie: InterPro:IPR027417
      label: P-loop containing nucleoside triphosphate hydrolase
      negated: false
    notes: Both signatures are DEAD-box RNA helicase features; helicases are ATP hydrolases.
  - number: 2
    conditions:
    - condition_type: INTERPRO
      value: IPR033704
      curie: InterPro:IPR033704
      label: dUTPase, trimeric
      negated: false
    - condition_type: INTERPRO
      value: IPR036157
      curie: InterPro:IPR036157
      label: dUTPase-like superfamily
      negated: false
    notes: dUTPase (EC 3.6.1.23) signatures.
  - number: 3
    conditions:
    - condition_type: INTERPRO
      value: IPR000629
      curie: InterPro:IPR000629
      label: ATP-dependent RNA helicase DEAD-box, conserved site
      negated: false
    - condition_type: INTERPRO
      value: IPR001650
      curie: InterPro:IPR001650
      label: Helicase, C-terminal domain-like
      negated: false
    - condition_type: INTERPRO
      value: IPR011545
      curie: InterPro:IPR011545
      label: DEAD/DEAH-box helicase domain
      negated: false
    notes: DEAD-box helicase conserved site with both helicase core domains.
  - number: 4
    conditions:
    - condition_type: INTERPRO
      value: IPR000672
      curie: InterPro:IPR000672
      label: Tetrahydrofolate dehydrogenase/cyclohydrolase
      negated: false
    - condition_type: INTERPRO
      value: IPR020630
      curie: InterPro:IPR020630
      label: Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain
      negated: false
    - condition_type: PANTHER
      value: PTHR48099:SF5
      curie: PANTHER:PTHR48099:SF5
      label: C-1-TETRAHYDROFOLATE SYNTHASE, CYTOPLASMIC
      negated: false
    notes: >-
      Tetrahydrofolate dehydrogenase/cyclohydrolase family with its catalytic domain and a PANTHER
      subfamily; the cyclohydrolase half is EC 3.5.4.9.
  go_annotations: []
  entries: []
  reviewed_protein_count: 0
  unreviewed_protein_count: 10279889
  created_date: '2020-05-12'
  modified_date: '2026-07-18'
  retrieved_date: '2026-11-09'
  source_condition_set_count: 4171
review_summary: >-
  The live rule has 4171 condition sets and UniProt reports 10,279,889 unreviewed proteins for it.
  Four sets (1-4) were examined: by the official InterPro names they describe DEAD-box helicases,
  dUTPase and the tetrahydrofolate dehydrogenase/cyclohydrolase family, all of which are hydrolases.
  No false positive has been identified. 4167 sets were not examined, so no verdict is given.
action: UNDECIDED
action_rationale: >-
  Only 4 of 4171 condition sets were examined, and all four are sound. Nothing verified shows a wrong
  annotation, and nothing verified covers the rest of the rule.
suggested_modifications:
- >-
  Examine a sample of condition sets against Swiss-Prot keyword use before recommending any change.
annotation_assessments:
- annotation_kind: KEYWORD
  value: KW-0378
  label: Hydrolase
  assessment: UNDECIDED
  matched_protein_count: 10279889
  notes: >-
    matched_protein_count is the unreviewedProteinCount reported by rest.uniprot.org/arba/ARBA00022801
    on 2026-11-09. Sets 1-4 name hydrolase families by their official InterPro names (IPR014014, IPR027417,
    IPR033704, IPR036157, IPR000629, IPR001650, IPR011545, IPR000672, IPR020630). No individual protein
    was checked.
corrections:
- date: '2026-11-10'
  withdrawn_claim: The rule includes non-hydrolytic domains (kinases, GTPase-activating proteins).
  correction: >-
    The four recorded condition sets carried wrong InterPro names. With the official names all four
    describe hydrolases, so no non-hydrolytic family has been shown in the rule.
  error_type: WRONG_IDENTIFIER_MEANING
  evidence:
  - >-
    InterPro API: IPR014014 = RNA helicase, DEAD-box type, Q motif (was labelled Beta-lactamase class
    A)
  - >-
    InterPro API: IPR033704 = dUTPase, trimeric; IPR036157 = dUTPase-like superfamily (were labelled
    beta-lactamase entries)
  - >-
    InterPro API: IPR000629 = ATP-dependent RNA helicase DEAD-box, conserved site (was labelled ATP/GTP-binding
    site motif A)
  - >-
    InterPro API: IPR000672 = Tetrahydrofolate dehydrogenase/cyclohydrolase; IPR020630 = Tetrahydrofolate
    dehydrogenase/cyclohydrolase, catalytic domain (were labelled GTPase-activating protein and Tyrosine-protein
    kinase, catalytic domain)
- date: '2026-11-10'
  withdrawn_claim: 4070 condition sets make the rule unmanageable and it should be removed.
  correction: >-
    The number of condition sets says nothing about whether the keyword is correct for the matched
    proteins.
  error_type: SIZE_AS_EVIDENCE
  evidence:
  - 'rest.uniprot.org/arba/ARBA00022801, 2026-11-09: 4171 condition sets'
- date: '2026-11-10'
  withdrawn_claim: The rule likely produces more false positives than useful annotations.
  correction: >-
    No false positive was identified; only four condition sets had been read, and the fourth was recorded
    without its PANTHER condition.
  error_type: UNEXAMINED_RULE
  evidence:
  - 'Live set 4: IPR000672 AND IPR020630 AND PTHR48099:SF5'
- date: '2026-11-10'
  withdrawn_claim: Literature contradicts the rule.
  correction: >-
    The only sources were the review's own notes and two papers that do not discuss this rule; the
    literature assessment is removed.
  error_type: UNSUPPORTED_SOURCE
  evidence:
  - No publication on ARBA00022801 or on KW-0378 assignment was cited
- date: '2026-11-10'
  withdrawn_claim: The rule covers 0 proteins.
  correction: UniProt reports 10,279,889 unreviewed proteins for the rule.
  error_type: STALE_RULE_VERSION
  evidence:
  - rest.uniprot.org/arba/ARBA00022801 statistics, 2026-11-09