ARBA00022759

id: ARBA00022759
description: >-
  Assigns the UniProt keyword Endonuclease (KW-0255) through 320 alternative condition sets. Each
  set is one to three InterPro entries or PANTHER families, in about a third of the sets with a taxon.
status: IN_PROGRESS
rule_type: ARBA
rule:
  rule_id: ARBA00022759
  condition_sets:
  - number: 1
    conditions:
    - condition_type: INTERPRO
      value: IPR001352
      curie: InterPro:IPR001352
      label: Ribonuclease HII/HIII
      negated: false
    - condition_type: INTERPRO
      value: IPR012337
      curie: InterPro:IPR012337
      label: Ribonuclease H-like superfamily
      negated: false
    - condition_type: INTERPRO
      value: IPR024567
      curie: InterPro:IPR024567
      label: Ribonuclease HII/HIII domain
      negated: false
    notes: >-
      UniProtKB release 2026_04: 797 reviewed entries match this set; 797 of them carry keyword KW-0255.
      23379 unreviewed entries match.
  - number: 2
    conditions:
    - condition_type: INTERPRO
      value: IPR002036
      curie: InterPro:IPR002036
      label: Endoribonuclease YbeY
      negated: false
    - condition_type: INTERPRO
      value: IPR023091
      curie: InterPro:IPR023091
      label: Metalloprotease catalytic domain superfamily, predicted
      negated: false
    notes: >-
      UniProtKB release 2026_04: 711 reviewed entries match this set; 711 of them carry keyword KW-0255.
      19430 unreviewed entries match.
  - number: 3
    conditions:
    - condition_type: INTERPRO
      value: IPR002176
      curie: InterPro:IPR002176
      label: Crossover junction endodeoxyribonuclease RuvC
      negated: false
    - condition_type: PANTHER
      value: PTHR30194:SF3
      curie: PANTHER:PTHR30194:SF3
      label: CROSSOVER JUNCTION ENDODEOXYRIBONUCLEASE RUVC
      negated: false
    notes: >-
      UniProtKB release 2026_04: 546 reviewed entries match this set; 546 of them carry keyword KW-0255.
      15616 unreviewed entries match.
  - number: 4
    conditions:
    - condition_type: INTERPRO
      value: IPR000100
      curie: InterPro:IPR000100
      label: Ribonuclease P
      negated: false
    - condition_type: INTERPRO
      value: IPR014721
      curie: InterPro:IPR014721
      label: Small ribosomal subunit protein uS5 domain 2-type fold, subgroup
      negated: false
    - condition_type: INTERPRO
      value: IPR020568
      curie: InterPro:IPR020568
      label: Ribosomal protein uS5 domain 2-type superfamily
      negated: false
    notes: >-
      UniProtKB release 2026_04: 507 reviewed entries match this set; 507 of them carry keyword KW-0255.
      16815 unreviewed entries match.
  - number: 5
    conditions:
    - condition_type: INTERPRO
      value: IPR000999
      curie: InterPro:IPR000999
      label: Ribonuclease III domain
      negated: false
    - condition_type: INTERPRO
      value: IPR011907
      curie: InterPro:IPR011907
      label: Ribonuclease III
      negated: false
    - condition_type: INTERPRO
      value: IPR036389
      curie: InterPro:IPR036389
      label: Ribonuclease III, endonuclease domain superfamily
      negated: false
    notes: >-
      UniProtKB release 2026_04: 506 reviewed entries match this set; 506 of them carry keyword KW-0255.
      19942 unreviewed entries match.
  - number: 6
    conditions:
    - condition_type: INTERPRO
      value: IPR014720
      curie: InterPro:IPR014720
      label: Double-stranded RNA-binding domain
      negated: false
    - condition_type: PANTHER
      value: PTHR11207
      curie: PANTHER:PTHR11207
      label: RIBONUCLEASE III
      negated: false
    - condition_type: PANTHER
      value: PTHR11207:SF0
      curie: PANTHER:PTHR11207:SF0
      label: RIBONUCLEASE 3
      negated: false
    notes: >-
      UniProtKB release 2026_04: 486 reviewed entries match this set; 486 of them carry keyword KW-0255.
      19721 unreviewed entries match.
  - number: 10
    conditions:
    - condition_type: INTERPRO
      value: IPR043128
      curie: InterPro:IPR043128
      label: Reverse transcriptase/Diguanylate cyclase domain
      negated: false
    - condition_type: TAXON
      value: Pararnavirae
      curie: NCBITaxon:2732397
      label: Pararnavirae
      negated: false
    notes: >-
      UniProtKB release 2026_04: 204 reviewed entries match this set; 204 of them carry keyword KW-0255.
      30500 unreviewed entries match. Retroviral and pararetroviral polymerase polyproteins, which
      include RNase H.
  - number: 13
    conditions:
    - condition_type: INTERPRO
      value: IPR029060
      curie: InterPro:IPR029060
      label: PIN-like domain superfamily
      negated: false
    - condition_type: PANTHER
      value: PTHR11081:SF9
      curie: PANTHER:PTHR11081:SF9
      label: FLAP ENDONUCLEASE 1
      negated: false
    notes: >-
      UniProtKB release 2026_04: 188 reviewed entries match this set; 188 of them carry keyword KW-0255.
      5334 unreviewed entries match. PANTHER subfamily FLAP ENDONUCLEASE 1.
  - number: 35
    conditions:
    - condition_type: INTERPRO
      value: IPR009461
      curie: InterPro:IPR009461
      label: Non-structural protein NSP16, coronavirus-like
      negated: false
    - condition_type: INTERPRO
      value: IPR029063
      curie: InterPro:IPR029063
      label: S-adenosyl-L-methionine-dependent methyltransferase superfamily
      negated: false
    - condition_type: INTERPRO
      value: IPR043609
      curie: InterPro:IPR043609
      label: NendoU domain, nidovirus
      negated: false
    notes: >-
      UniProtKB release 2026_04: 35 reviewed entries match this set; 35 of them carry keyword KW-0255.
      942 unreviewed entries match.
  - number: 52
    conditions:
    - condition_type: INTERPRO
      value: IPR004601
      curie: InterPro:IPR004601
      label: UV-endonuclease UvdE
      negated: false
    - condition_type: INTERPRO
      value: IPR036237
      curie: InterPro:IPR036237
      label: Xylose isomerase-like superfamily
      negated: false
    - condition_type: PANTHER
      value: PTHR31290:SF5
      curie: PANTHER:PTHR31290:SF5
      label: UV-DAMAGE ENDONUCLEASE
      negated: false
    notes: >-
      UniProtKB release 2026_04: 21 reviewed entries match this set; 21 of them carry keyword KW-0255.
      3318 unreviewed entries match.
  - number: 97
    conditions:
    - condition_type: INTERPRO
      value: IPR036890
      curie: InterPro:IPR036890
      label: Histidine kinase/HSP90-like ATPase superfamily
      negated: false
    - condition_type: INTERPRO
      value: IPR041006
      curie: InterPro:IPR041006
      label: Morc, S5 domain 2-like
      negated: false
    - condition_type: TAXON
      value: Streptophyta
      curie: NCBITaxon:35493
      label: Streptophyta
      negated: false
    notes: >-
      UniProtKB release 2026_04: 7 reviewed entries match this set; 7 of them carry keyword KW-0255.
      3100 unreviewed entries match. Plant MORC family proteins.
  go_annotations: []
  entries: []
  reviewed_protein_count: 0
  unreviewed_protein_count: 565645
  created_date: '2020-05-12'
  modified_date: '2026-07-18'
  retrieved_date: '2026-11-09'
  source_condition_set_count: 320
review_summary: >-
  11 of the 320 live condition sets were examined: the first six and five that contain a domain shared
  with non-nuclease proteins. In each of the eleven, every reviewed match carries the Endonuclease
  keyword (4008 of 4008, summed over sets). The five sets with a broadly shared domain each pair it
  with a signature for a known endonuclease: FEN1, the nidovirus NendoU domain, UV-damage endonuclease
  UvdE, plant MORC proteins and retroviral polymerase polyproteins. The remaining 309 sets were not
  examined.
action: UNDECIDED
action_rationale: >-
  The rule was sampled, not examined set by set, so no verdict is given. The sampled sets are sound,
  which removes the grounds of the earlier verdict but does not establish that every set is right.
  The counts are from Swiss-Prot, which is also what ARBA learns its rules from, so they show the
  condition sets are coherent rather than giving an independent error rate for unreviewed entries.
annotation_assessments:
- annotation_kind: KEYWORD
  value: KW-0255
  label: Endonuclease
  assessment: UNDECIDED
  correct_examples:
  - P0A898
  - P58557
  - P39749
  - Q10988
  - Q84WV6
  notes: >-
    UniProtKB release 2026_04, reviewed entries matching a set and carrying KW-0255: set 2, P0A898
    (Escherichia coli ybeY) and P58557 (human YBEY); set 13, P39749 (mouse Fen1); set 52, Q10988 (Schizosaccharomyces
    pombe uve1); set 97, Q84WV6 (Arabidopsis MORC1). Per-set counts are in the condition set notes.
corrections:
- date: '2026-11-10'
  withdrawn_claim: >-
    A condition set combines the SRP54-type GTPase domain with a ribosomal protein S30AE signature;
    these are ribosomal and signal recognition particle domains, not endonucleases, and show the rule
    produces false positives.
  correction: >-
    Both identifiers were given the names of other entries. The set is IPR002036 (Endoribonuclease
    YbeY) AND IPR023091 (Metalloprotease catalytic domain superfamily, predicted), which selects the
    YbeY endoribonuclease family.
  error_type: WRONG_IDENTIFIER_MEANING
  evidence:
  - >-
    InterPro API: IPR002036 name Endoribonuclease YbeY; IPR023091 name Metalloprotease catalytic domain
    superfamily, predicted.
  - >-
    UniProtKB release 2026_04: 711 reviewed entries match set 2 and all 711 carry keyword KW-0255,
    for example P0A898 and P58557.
- date: '2026-11-10'
  withdrawn_claim: IPR001352 is a papain-like protease domain entry.
  correction: IPR001352 is the Ribonuclease HII/HIII family; set 1 selects RNase HII and HIII.
  error_type: WRONG_IDENTIFIER_MEANING
  evidence:
  - 'InterPro API: IPR001352 name Ribonuclease HII/HIII.'
  - 'UniProtKB release 2026_04: 797 reviewed entries match set 1 and all carry keyword KW-0255.'
- date: '2026-11-10'
  withdrawn_claim: >-
    Several domains in the rule belong to non-nuclease proteins (SAM-dependent methyltransferases,
    histidine kinases, xylose isomerases, PIN-like domains), so the rule annotates non-nucleases.
  correction: >-
    Each of those domains occurs only inside a conjunction with a signature specific to an endonuclease.
    The domain was judged alone, without the other conditions of its set.
  error_type: CONJUNCTION_IGNORED
  evidence:
  - >-
    Set 35: IPR009461 AND IPR029063 AND IPR043609 (NendoU domain, nidovirus); 35 of 35 reviewed matches
    carry KW-0255.
  - >-
    Set 52: IPR004601 (UV-endonuclease UvdE) AND IPR036237 AND PANTHER:PTHR31290:SF5; 21 of 21.
  - 'Set 13: IPR029060 AND PANTHER:PTHR11081:SF9, FLAP ENDONUCLEASE 1; 188 of 188.'
  - >-
    Set 97: IPR036890 AND IPR041006 AND taxon Streptophyta; 7 of 7, for example Q84WV6 (MORC1).
- date: '2026-11-10'
  withdrawn_claim: >-
    The rule must be removed because 318 condition sets make it impossible to review and the Endonuclease
    category is too broad to be meaningful.
  correction: >-
    The number of sets is not evidence of error, and a broad keyword that is true of a protein is
    not a wrong annotation. No protein wrongly given the keyword was identified.
  error_type: SIZE_AS_EVIDENCE
  evidence:
  - >-
    UniProt ARBA API, ARBA00022759, retrieved 2026-11-09: 320 condition sets, 222 of them conjunctions
    of two or three conditions.
- date: '2026-11-10'
  withdrawn_claim: The rule is deficient because it assigns a keyword and not GO terms.
  correction: >-
    The rule's consequent is a UniProt keyword by design. The absence of a GO term is not a defect
    of a keyword rule.
  error_type: OTHER
  evidence:
  - 'UniProt ARBA API, ARBA00022759: single annotation, keyword KW-0255 Endonuclease.'
- date: '2026-11-10'
  withdrawn_claim: The literature contradicts the rule.
  correction: >-
    The only sources given were the review's own research notes, which describe diversity among nucleases.
    No publication was cited that shows a matched protein is not an endonuclease.
  error_type: UNSUPPORTED_SOURCE
  evidence:
  - >-
    The old literature_support block cited only rules/arba/ARBA00022759/ARBA00022759-deep-research-manual.md.