ARBA00089180 cellular response to lectin (GO:1990858)

View original ARBA rule on UniProt

Type: ARBA
Status: COMPLETE
Action: MODIFY
Confidence: 0.60

Description

Assigns GO:1990858 cellular response to lectin through two alternative condition sets of CATH FunFams with a taxon: a pair of FunFams that together select group I p21-activated kinases (PAK1, PAK2, PAK3) in Primates, and a pair that selects CREBBP and EP300 in Catarrhini.

Analysis Summary

Condition-set counts describe the sets recorded in this review, which may omit the full rule.

2
Domain Pairs Analyzed
2
Recorded condition sets
1
Subset Relationships
0
Redundant Annotations

No domain overlap table is shown: the cached overlap analysis for this version of the review is not available. Run just analyze-rule ARBA00089180 and re-render to add it.

Review Summary

Both live condition sets were examined. Set 1 matches five primate Swiss-Prot entries, all PAK1, PAK2 or PAK3; set 2 matches human CREBBP and EP300. The five human proteins are annotated by Reactome (TAS, R-HSA-5621481) to GO:0002223 stimulatory C-type lectin receptor signaling pathway, a child of the rule's term. There is no experimental GO evidence for the term on any matched protein, and the rule assigns the parent rather than the curated child.

Action Rationale

The rule propagates a curated pathway annotation from the human proteins to their primate orthologs, so it is not producing false positives among the proteins it selects. Its consequent is less specific than the curated annotation it rests on.

GO Annotations

GO:1990858 - cellular response to lectin
Aspect: BP

Annotation Assessments

TOO_GENERAL GO_TERM GO:1990858 - cellular response to lectin
Matched proteins: ; incorrect:
Correct examples: Q13153, Q13177, O75914, Q92793, Q09472

Each listed accession carries GO:0002223 stimulatory C-type lectin receptor signaling pathway, TAS, Reactome:R-HSA-5621481, which entails GO:1990858. The two other Swiss-Prot matches of set 1 (Q7YQL4 PAK3_PANTR, Q7YQL3 PAK3_PONPY) have the term by IEA only.

Rule Definition

Condition Sets

Condition Set 1

3 condition(s)
Notes:

UniProtKB query, November 2026: 5 Swiss-Prot and 213 TrEMBL entries match. QuickGO, GO:1990858 or a descendant on the Swiss-Prot entries: 0 with experimental evidence, 3 with other manual evidence only, 2 with IEA only, 0 with none. Examples: Q13177 (PAK2_HUMAN) GO:0002223 stimulatory C-type lectin receptor signaling pathway, TAS, Reactome:R-HSA-5621481; O75914 (PAK3_HUMAN) GO:0002223 stimulatory C-type lectin receptor signaling pathway, TAS, Reactome:R-HSA-5621481.

Pairwise Overlap Analysis

Condition A Condition B Count A Count B Intersection Jaccard A in B B in A Interpretation
1.10.510.10:FF:000011 3.30.200.20:FF:000069 33 15 15 0.455 0.455 1.000 SUBSET

Condition Set 2

3 condition(s)
Notes:

UniProtKB query, November 2026: 2 Swiss-Prot and 103 TrEMBL entries match. QuickGO, GO:1990858 or a descendant on the Swiss-Prot entries: 0 with experimental evidence, 2 with other manual evidence only, 0 with IEA only, 0 with none. Examples: Q92793 (CBP_HUMAN) GO:0002223 stimulatory C-type lectin receptor signaling pathway, TAS, Reactome:R-HSA-5621481; Q09472 (EP300_HUMAN) GO:0002223 stimulatory C-type lectin receptor signaling pathway, TAS, Reactome:R-HSA-5621481.

Pairwise Overlap Analysis

Condition A Condition B Count A Count B Intersection Jaccard A in B B in A Interpretation
1.10.246.20:FF:000001 1.20.1020.10:FF:000001 5 5 5 1.000 1.000 1.000 REDUNDANT

Assessments

WEAK

The only manual support is a Reactome pathway-membership statement: Q13153 (PAK1), Q13177 (PAK2), O75914 (PAK3), Q92793 (CREBBP) and Q09472 (EP300) each carry GO:0002223, TAS, Reactome:R-HSA-5621481 (QuickGO, November 2026). No experimental annotation to GO:1990858 or a descendant exists on these proteins.

TOO_BROAD

The curated annotations on all matched human proteins are to GO:0002223, an is_a descendant of GO:1990858 (QuickGO).

Raw YAML

View Source YAML 
id: ARBA00089180
description: 'Assigns GO:1990858 cellular response to lectin through two alternative condition sets of
  CATH FunFams with a taxon: a pair of FunFams that together select group I p21-activated kinases (PAK1,
  PAK2, PAK3) in Primates, and a pair that selects CREBBP and EP300 in Catarrhini.'
status: COMPLETE
rule_type: ARBA
rule:
  rule_id: ARBA00089180
  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: 'UniProtKB query, November 2026: 5 Swiss-Prot and 213 TrEMBL entries match. QuickGO, GO:1990858
      or a descendant on the Swiss-Prot entries: 0 with experimental evidence, 3 with other manual evidence
      only, 2 with IEA only, 0 with none. Examples: Q13177 (PAK2_HUMAN) GO:0002223 stimulatory C-type
      lectin receptor signaling pathway, TAS, Reactome:R-HSA-5621481; O75914 (PAK3_HUMAN) GO:0002223 stimulatory
      C-type lectin receptor signaling pathway, TAS, Reactome:R-HSA-5621481.'
    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: 'UniProtKB query, November 2026: 2 Swiss-Prot and 103 TrEMBL entries match. QuickGO, GO:1990858
      or a descendant on the Swiss-Prot entries: 0 with experimental evidence, 2 with other manual evidence
      only, 0 with IEA only, 0 with none. Examples: Q92793 (CBP_HUMAN) GO:0002223 stimulatory C-type lectin
      receptor signaling pathway, TAS, Reactome:R-HSA-5621481; Q09472 (EP300_HUMAN) GO:0002223 stimulatory
      C-type lectin receptor signaling pathway, TAS, Reactome:R-HSA-5621481.'
    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:1990858
    go_label: cellular 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:1990858
      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:1990858
      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:1990858
      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:1990858
      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 matches five primate Swiss-Prot entries,
  all PAK1, PAK2 or PAK3; set 2 matches human CREBBP and EP300. The five human proteins are annotated
  by Reactome (TAS, R-HSA-5621481) to GO:0002223 stimulatory C-type lectin receptor signaling pathway,
  a child of the rule's term. There is no experimental GO evidence for the term on any matched protein,
  and the rule assigns the parent rather than the curated child.
action: MODIFY
action_rationale: The rule propagates a curated pathway annotation from the human proteins to their primate
  orthologs, so it is not producing false positives among the proteins it selects. Its consequent is less
  specific than the curated annotation it rests on.
suggested_modifications:
- Replace the consequent GO:1990858 cellular response to lectin with GO:0002223 stimulatory C-type lectin
  receptor signaling pathway, the term the human members carry (Reactome:R-HSA-5621481).
literature_support:
  assessment: WEAK
  notes: 'The only manual support is a Reactome pathway-membership statement: Q13153 (PAK1), Q13177 (PAK2),
    O75914 (PAK3), Q92793 (CREBBP) and Q09472 (EP300) each carry GO:0002223, TAS, Reactome:R-HSA-5621481
    (QuickGO, November 2026). No experimental annotation to GO:1990858 or a descendant exists on these
    proteins.'
go_specificity:
  assessment: TOO_BROAD
  notes: The curated annotations on all matched human proteins are to GO:0002223, an is_a descendant of
    GO:1990858 (QuickGO).
annotation_assessments:
- annotation_kind: GO_TERM
  value: GO:1990858
  label: cellular response to lectin
  assessment: TOO_GENERAL
  correct_examples:
  - Q13153
  - Q13177
  - O75914
  - Q92793
  - Q09472
  notes: Each listed accession carries GO:0002223 stimulatory C-type lectin receptor signaling pathway,
    TAS, Reactome:R-HSA-5621481, which entails GO:1990858. The two other Swiss-Prot matches of set 1 (Q7YQL4
    PAK3_PANTR, Q7YQL3 PAK3_PONPY) have the term by IEA only.
confidence: 0.6
corrections:
- date: '2026-11-10'
  withdrawn_claim: Condition set 1 is general serine/threonine kinase machinery; the rule annotates all
    proteins with serine/threonine kinase domains. RAF1 is the relevant kinase.
  correction: The FunFam label is an enzyme-class name, not a description of breadth. The two-FunFam conjunction
    matches 15 Swiss-Prot proteins, all group I p21-activated kinases; RAF1 is not matched.
  error_type: CONJUNCTION_IGNORED
  evidence:
  - 'UniProtKB query (xref:"funfam-1.10.510.10:FF:000011") AND (xref:"funfam-3.30.200.20:FF:000069") AND
    (reviewed:true): 15 entries, all PAK1/PAK2/PAK3 orthologs plus PAK_DROME'
  - 'With (taxonomy_id:9443): Q13153, Q13177, O75914, Q7YQL4, Q7YQL3'
- date: '2026-11-10'
  withdrawn_claim: Only 9 to 40 percent of proteins with these FunFams have the GO term, so most matched
    proteins do not have lectin response as a function.
  correction: Those fractions were computed per FunFam over all taxa. Within the rule's taxon conditions,
    every human Swiss-Prot match carries a curated child term; the non-primate orthologs that lower the
    fraction are outside the rule.
  error_type: LOW_RECALL_IS_NOT_WRONG
  evidence:
  - 'Q13153, Q13177, O75914, Q92793, Q09472: GO:0002223, TAS, Reactome:R-HSA-5621481'
  - GO:0002223 is_a descendant of GO:1990858 (QuickGO)
- date: '2026-11-10'
  withdrawn_claim: The literature contradicts the rule.
  correction: The cited source was a machine-generated research summary, and the same passage states that
    these proteins take part in C-type lectin receptor signaling. No publication contradicting the annotation
    was identified.
  error_type: UNSUPPORTED_SOURCE
  evidence:
  - Old literature_support cited only ARBA00089180-deep-research-perplexity.md
- date: '2026-11-10'
  withdrawn_claim: The two condition sets are completely disjoint, which violates biological coherence,
    and the two FunFams of set 2 are redundant; both are grounds for deprecation.
  correction: Alternative sets are expected to match different proteins, and a redundant condition within
    a set does not change which proteins are annotated.
  error_type: OTHER
  evidence:
  - 'Set 2 pairwise overlap: both FunFams match the same 5 Swiss-Prot entries (rule.condition_sets[1].pairwise_overlap)'