ARBA00089176 response to lectin (GO:1990840)

id: ARBA00089176
description: >-
  ARBA rule assigning GO:1990840 response to lectin through two condition sets: two PAK-family kinase
  FunFams in Primates, and two p300/CBP FunFams in Catarrhini.
status: COMPLETE
rule_type: ARBA
rule:
  rule_id: ARBA00089176
  condition_sets:
  - number: 1
    conditions:
    - condition_type: FUNFAM
      value: 1.10.510.10:FF:000011
      curie: CATH.FunFam:1.10.510.10:FF:000011
      label: Non-specific serine/threonine protein kinase
      negated: false
    - condition_type: FUNFAM
      value: 3.30.200.20:FF:000069
      curie: CATH.FunFam:3.30.200.20:FF:000069
      label: Non-specific serine/threonine protein kinase
      negated: false
    - condition_type: TAXON
      value: '9443'
      curie: NCBITaxon:9443
      label: Primates
      negated: false
    notes: >-
      PAK family kinases in Primates. In Swiss-Prot the conjunction matches five proteins: human PAK1
      (Q13153), PAK2 (Q13177) and PAK3 (O75914), and PAK3 of chimpanzee (Q7YQL4) and orangutan (Q7YQL3).
      The 33 and 15 protein counts below are for each FunFam alone, without the taxon condition.
    pairwise_overlap:
    - condition_a: 1.10.510.10:FF:000011
      condition_b: 3.30.200.20:FF:000069
      protein_database: SWISSPROT
      count_a: 33
      count_b: 15
      intersection_count: 15
      a_minus_b_count: 18
      b_minus_a_count: 0
      jaccard_similarity: 0.45454545454545453
      containment_a_in_b: 0.45454545454545453
      containment_b_in_a: 1.0
      interpretation: SUBSET
  - number: 2
    conditions:
    - condition_type: FUNFAM
      value: 1.10.246.20:FF:000001
      curie: CATH.FunFam:1.10.246.20:FF:000001
      label: E1A binding protein p300
      negated: false
    - condition_type: FUNFAM
      value: 1.20.1020.10:FF:000001
      curie: CATH.FunFam:1.20.1020.10:FF:000001
      label: E1A binding protein p300
      negated: false
    - condition_type: TAXON
      value: '9526'
      curie: NCBITaxon:9526
      label: Catarrhini
      negated: false
    notes: >-
      p300/CBP in Catarrhini. Of the five Swiss-Prot proteins that carry both FunFams, the two catarrhine
      ones are human EP300 (Q09472) and CREBBP (Q92793); the others are mouse and rat.
    pairwise_overlap:
    - condition_a: 1.10.246.20:FF:000001
      condition_b: 1.20.1020.10:FF:000001
      protein_database: SWISSPROT
      count_a: 5
      count_b: 5
      intersection_count: 5
      a_minus_b_count: 0
      b_minus_a_count: 0
      jaccard_similarity: 1.0
      containment_a_in_b: 1.0
      containment_b_in_a: 1.0
      interpretation: REDUNDANT
  go_annotations:
  - go_id: GO:1990840
    go_label: response to lectin
    aspect: BP
  entries:
  - id: 1.10.246.20:FF:000001
    type: FUNFAM
    label: E1A binding protein p300
    appears_in_condition_sets:
    - 2
    protein_count: 5
    related_entries:
    - relationship: EQUIV
      target_id: 1.10.510.10:FF:000011
      containment: 0.0
      jaccard_similarity: 0.0
      intersection_count: 0
      exclusive_count: 5
    - relationship: EQUIV
      target_id: 3.30.200.20:FF:000069
      containment: 0.0
      jaccard_similarity: 0.0
      intersection_count: 0
      exclusive_count: 5
    - relationship: EQUIV
      target_id: 1.20.1020.10:FF:000001
      containment: 1.0
      jaccard_similarity: 1.0
      intersection_count: 5
      exclusive_count: 0
    - relationship: PREDICTS
      target_id: GO:1990840
      containment: 0.4
      jaccard_similarity: 0.032
      intersection_count: 2
      exclusive_count: 3
  - id: 1.10.510.10:FF:000011
    type: FUNFAM
    label: Non-specific serine/threonine protein kinase
    appears_in_condition_sets:
    - 1
    protein_count: 33
    related_entries:
    - relationship: PREDICTED_BY
      target_id: 3.30.200.20:FF:000069
      containment: 1.0
      jaccard_similarity: 0.455
      intersection_count: 15
      exclusive_count: 0
    - relationship: EQUIV
      target_id: 1.10.246.20:FF:000001
      containment: 0.0
      jaccard_similarity: 0.0
      intersection_count: 0
      exclusive_count: 33
    - relationship: EQUIV
      target_id: 1.20.1020.10:FF:000001
      containment: 0.0
      jaccard_similarity: 0.0
      intersection_count: 0
      exclusive_count: 33
    - relationship: PREDICTS
      target_id: GO:1990840
      containment: 0.091
      jaccard_similarity: 0.034
      intersection_count: 3
      exclusive_count: 30
  - id: 1.20.1020.10:FF:000001
    type: FUNFAM
    label: E1A binding protein p300
    appears_in_condition_sets:
    - 2
    protein_count: 5
    related_entries:
    - relationship: EQUIV
      target_id: 1.10.510.10:FF:000011
      containment: 0.0
      jaccard_similarity: 0.0
      intersection_count: 0
      exclusive_count: 5
    - relationship: EQUIV
      target_id: 3.30.200.20:FF:000069
      containment: 0.0
      jaccard_similarity: 0.0
      intersection_count: 0
      exclusive_count: 5
    - relationship: EQUIV
      target_id: 1.10.246.20:FF:000001
      containment: 1.0
      jaccard_similarity: 1.0
      intersection_count: 5
      exclusive_count: 0
    - relationship: PREDICTS
      target_id: GO:1990840
      containment: 0.4
      jaccard_similarity: 0.032
      intersection_count: 2
      exclusive_count: 3
  - id: 3.30.200.20:FF:000069
    type: FUNFAM
    label: Non-specific serine/threonine protein kinase
    appears_in_condition_sets:
    - 1
    protein_count: 15
    related_entries:
    - relationship: PREDICTS
      target_id: 1.10.510.10:FF:000011
      containment: 0.455
      jaccard_similarity: 0.455
      intersection_count: 15
      exclusive_count: 18
    - relationship: EQUIV
      target_id: 1.10.246.20:FF:000001
      containment: 0.0
      jaccard_similarity: 0.0
      intersection_count: 0
      exclusive_count: 15
    - relationship: EQUIV
      target_id: 1.20.1020.10:FF:000001
      containment: 0.0
      jaccard_similarity: 0.0
      intersection_count: 0
      exclusive_count: 15
    - relationship: PREDICTS
      target_id: GO:1990840
      containment: 0.2
      jaccard_similarity: 0.042
      intersection_count: 3
      exclusive_count: 12
  reviewed_protein_count: 0
  unreviewed_protein_count: 0
  created_date: '2025-03-21'
  modified_date: '2025-03-21'
  retrieved_date: '2026-11-09'
  source_condition_set_count: 2
review_summary: >-
  Both live condition sets were examined. Set 1 selects PAK kinases in Primates and set 2 selects
  p300/CBP in Catarrhini. All five human proteins they match (PAK1, PAK2, PAK3, EP300, CREBBP) carry
  GO:0002223 stimulatory C-type lectin receptor signaling pathway, a descendant of GO:1990840, as
  a Reactome traceable author statement (R-HSA-5621481). The other two Swiss-Prot matches are ape
  PAK3 orthologues. The rule therefore extends a curated human pathway annotation to primate orthologues,
  using the parent term.
action: ACCEPT
action_rationale: >-
  Each condition set matches only the proteins, or primate orthologues of the proteins, that curators
  have annotated to a descendant of the rule's term. The support is pathway membership recorded by
  Reactome, not an experiment on lectin response, which is why confidence is moderate.
suggested_modifications:
- >-
  Optional refinement: assert GO:0002223 stimulatory C-type lectin receptor signaling pathway, the
  term the curated annotations use, instead of its ancestor GO:1990840.
literature_support:
  assessment: MODERATE
  notes: >-
    Curated database support only: Reactome pathway R-HSA-5621481 is the source of the TAS annotations
    of human PAK1, PAK2, PAK3, EP300 and CREBBP to GO:0002223. No experimental GO annotation to GO:1990840
    or GO:0002223 exists for these proteins in QuickGO.
condition_overlap:
  assessment: NONE
  notes: >-
    The two condition sets share no protein (recorded Swiss-Prot intersection counts of 0 between
    the kinase and p300 FunFams). Within set 2 the two FunFams co-occur in the same five proteins.
go_specificity:
  assessment: TOO_BROAD
  notes: >-
    The curated annotations of the matched human proteins are to GO:0002223, a descendant of GO:1990840.
    The rule's term is true of them but less specific.
taxonomic_scope:
  assessment: APPROPRIATE
  notes: >-
    Primates for set 1 and Catarrhini for set 2 keep the matches to the annotated human proteins and
    their close orthologues.
annotation_assessments:
- annotation_kind: GO_TERM
  value: GO:1990840
  label: response to lectin
  assessment: TOO_GENERAL
  matched_protein_count: 7
  correct_examples:
  - Q13153
  - Q13177
  - O75914
  - Q09472
  - Q92793
  notes: >-
    matched_protein_count is the number of Swiss-Prot entries matching either conjunction (UniProtKB
    query 2026-11-09: 5 for set 1 with taxonomy 9443; CBP_HUMAN and EP300_HUMAN for set 2). QuickGO:
    PAK1, PAK2, PAK3, EP300 and CREBBP (human) each have GO:0002223, TAS, Reactome:R-HSA-5621481.
    GO:0002223 has GO:1990840 as an ancestor.
confidence: 0.6
corrections:
- date: '2026-11-10'
  withdrawn_claim: >-
    Only 3 of 33 kinase proteins and 2 of 5 p300 proteins carry the term, so the rule has poor predictive
    accuracy (3-40%).
  correction: >-
    Those ratios are for single FunFams with the taxon condition left out. With the full conjunctions
    every matched human protein is annotated to a descendant term and the remaining matches are primate
    orthologues.
  error_type: CONJUNCTION_IGNORED
  evidence:
  - >-
    UniProtKB query xref funfam-3.30.200.20:FF:000069 AND funfam-1.10.510.10:FF:000011 AND reviewed
    AND taxonomy 9443: 5 entries (PAK1_HUMAN, PAK2_HUMAN, PAK3_HUMAN, PAK3_PANTR, PAK3_PONPY)
  - >-
    UniProtKB query xref funfam-1.10.246.20:FF:000001 AND reviewed: CBP_HUMAN, EP300_HUMAN, EP300_MOUSE,
    CBP_MOUSE, CBP_RAT
  - 'QuickGO: Q13153, Q13177, O75914, Q09472, Q92793 GO:0002223 TAS Reactome:R-HSA-5621481'
- date: '2026-11-10'
  withdrawn_claim: Condition set 1 targets RAF1, which acts downstream of DC-SIGN.
  correction: RAF1 is not in either FunFam of set 1; the set selects the PAK family.
  error_type: WRONG_IDENTIFIER_MEANING
  evidence:
  - 'UniProtKB P04049 (RAF1_HUMAN) FunFams: 1.10.510.10:FF:000036, 3.30.200.20:FF:000024'
  - 'UniProtKB Q13153 (PAK1_HUMAN) FunFams: 1.10.510.10:FF:000011, 3.30.200.20:FF:000069'
- date: '2026-11-10'
  withdrawn_claim: >-
    The kinase and p300 domains are shared by hundreds of proteins, creating high false positive risk.
  correction: >-
    The FunFams used hold 33, 15 and 5 Swiss-Prot proteins, and the taxon conditions cut the matches
    to seven. No false positive was named.
  error_type: SAMPLE_OVERGENERALISED
  evidence:
  - >-
    Recorded Swiss-Prot counts: 1.10.510.10:FF:000011 = 33; 3.30.200.20:FF:000069 = 15; both p300
    FunFams = 5
- date: '2026-11-10'
  withdrawn_claim: >-
    The Primates and Catarrhini restrictions are too narrow and should be widened to Mammalia or Vertebrata.
  correction: >-
    The restriction keeps the rule to close orthologues of the annotated human proteins; no evidence
    was given that the annotation holds, or is wanted, for more distant members.
  error_type: TAXON_MISREAD
  evidence:
  - Curated support is on human proteins only (Reactome:R-HSA-5621481)
- date: '2026-11-10'
  withdrawn_claim: Deep-research text on RAF1 and p65 acetylation supports a weak literature assessment.
  correction: >-
    Those passages came from generated research notes, not from checked publications, and described
    a different kinase; they are removed.
  error_type: UNSUPPORTED_SOURCE
  evidence:
  - Previous supported_by cited ARBA00089176-deep-research-perplexity.md and -falcon.md only