ARBA00001712

id: ARBA00001712
description: 'Assigns the catalytic activity alpha-D-galactose = beta-D-galactose (RHEA:28675, EC 5.1.3.3, galactose
  mutarotase) through two alternative condition sets: InterPro IPR008183 and IPR011013 in Metazoa, or CATH FunFam
  2.70.98.10:FF:000003 in Eukaryota.'
status: COMPLETE
rule_type: ARBA
rule:
  rule_id: ARBA00001712
  condition_sets:
  - number: 1
    conditions:
    - condition_type: INTERPRO
      value: IPR008183
      curie: InterPro:IPR008183
      label: Aldose 1-/Glucose-6-phosphate 1-epimerase
      interpro_type: FAMILY
      negated: false
    - condition_type: INTERPRO
      value: IPR011013
      curie: InterPro:IPR011013
      label: Galactose mutarotase-like domain superfamily
      interpro_type: HOMOLOGOUS_SUPERFAMILY
      negated: false
    - condition_type: TAXON
      value: Metazoa
      curie: NCBITaxon:33208
      label: Metazoa
      negated: false
    notes: 'Swiss-Prot entries matching this set (2026-11-09): 6. 6 carry EC 5.1.3.3. UniProtKB entries matching:
      2715.'
    pairwise_overlap:
    - condition_a: IPR008183
      condition_b: IPR011013
      protein_database: SWISSPROT
      count_a: 31
      count_b: 397
      intersection_count: 31
      a_minus_b_count: 0
      b_minus_a_count: 366
      jaccard_similarity: 0.07808564231738035
      containment_a_in_b: 1.0
      containment_b_in_a: 0.07808564231738035
      interpretation: SUBSET
  - number: 2
    conditions:
    - condition_type: FUNFAM
      value: 2.70.98.10:FF:000003
      curie: CATH.FunFam:2.70.98.10:FF:000003
      label: Aldose 1-epimerase
      negated: false
    - condition_type: TAXON
      value: Eukaryota
      curie: NCBITaxon:2759
      label: Eukaryota
      negated: false
    notes: 'Swiss-Prot entries matching this set (2026-11-09): 6. 6 carry EC 5.1.3.3. UniProtKB entries matching:
      1187.'
  catalytic_activity_annotations:
  - reaction_name: alpha-D-galactose = beta-D-galactose
    rhea_id: RHEA:28675
    ec_number: 5.1.3.3
  entries:
  - id: 2.70.98.10:FF:000003
    type: FUNFAM
    label: Aldose 1-epimerase
    appears_in_condition_sets:
    - 2
    protein_count: 6
    related_entries:
    - relationship: PREDICTS
      target_id: IPR008183
      containment: 0.194
      jaccard_similarity: 0.194
      intersection_count: 6
      exclusive_count: 25
    - relationship: PREDICTS
      target_id: IPR011013
      containment: 0.015
      jaccard_similarity: 0.015
      intersection_count: 6
      exclusive_count: 391
  - id: IPR008183
    type: INTERPRO
    label: Aldose 1-/Glucose-6-phosphate 1-epimerase
    appears_in_condition_sets:
    - 1
    protein_count: 31
    related_entries:
    - relationship: PREDICTS
      target_id: IPR011013
      containment: 1.0
      jaccard_similarity: 0.078
      intersection_count: 31
      exclusive_count: 0
    - relationship: PREDICTED_BY
      target_id: 2.70.98.10:FF:000003
      containment: 1.0
      jaccard_similarity: 0.194
      intersection_count: 6
      exclusive_count: 0
  - id: IPR011013
    type: INTERPRO
    label: Galactose mutarotase-like domain superfamily
    appears_in_condition_sets:
    - 1
    protein_count: 397
    related_entries:
    - relationship: PREDICTED_BY
      target_id: IPR008183
      containment: 0.078
      jaccard_similarity: 0.078
      intersection_count: 31
      exclusive_count: 366
    - relationship: PREDICTED_BY
      target_id: 2.70.98.10:FF:000003
      containment: 1.0
      jaccard_similarity: 0.015
      intersection_count: 6
      exclusive_count: 0
  reviewed_protein_count: 0
  unreviewed_protein_count: 2727
  created_date: '2020-05-12'
  modified_date: '2025-03-21'
  retrieved_date: '2026-11-09'
  source_condition_set_count: 2
review_summary: 'Both live condition sets were checked against Swiss-Prot. Each matches six reviewed entries and
  all six carry EC 5.1.3.3 (GALM orthologues, e.g. human Q96C23). The Metazoa restriction in set 1 is needed: across
  all taxa IPR008183 has 32 Swiss-Prot members of which only 18 carry EC 5.1.3.3, the others including glucose-6-phosphate
  1-epimerases (EC 5.1.3.15, e.g. yeast Q03161) and the sulfoquinovose mutarotase P32139. Checked against Swiss-Prot
  by UniProtKB query on 2026-11-09; TrEMBL matches were counted but not inspected.'
action: ACCEPT
action_rationale: 'Every live condition set is supported: 6 of 6 Swiss-Prot matches of each set carry EC 5.1.3.3,
  and no reviewed match lacks it.'
parsimony:
  assessment: ACCEPTABLE
  notes: In set 1 IPR011013 is a homologous superfamily that contains every Swiss-Prot IPR008183 protein (31 of
    31 in the recorded pairwise overlap), so it does not narrow the set further. It does no harm.
taxonomic_scope:
  assessment: APPROPRIATE
  notes: 'IPR008183 (Aldose 1-/Glucose-6-phosphate 1-epimerase) is not specific to galactose mutarotase: 32 Swiss-Prot
    members, 18 with EC 5.1.3.3, 5 with EC 5.1.3.15. Within Metazoa 6 of 6 carry EC 5.1.3.3, so the taxon condition
    is what makes set 1 precise. Set 2 uses a narrower FunFam and can afford the wider taxon.'
annotation_assessments:
- annotation_kind: CATALYTIC_ACTIVITY
  value: RHEA:28675
  label: alpha-D-galactose = beta-D-galactose (EC 5.1.3.3)
  assessment: CORRECT
  correct_examples:
  - Q96C23
  - Q5EA79
  - Q66HG4
  - Q8K157
  - Q9GKX6
  - Q5R8U1
  notes: 'Set 1: 6 Swiss-Prot matches, 6 with EC 5.1.3.3. Set 2: 6 Swiss-Prot matches, 6 with EC 5.1.3.3. No reviewed
    match of either set lacks the EC number. UniProtKB matches: 2715 (set 1) and 1187 (set 2); the rule statistics
    report 2727 unreviewed proteins.'
confidence: 0.8
corrections:
- date: '2026-11-10'
  withdrawn_claim: The rule should be simplified to IPR008183 alone, and its taxonomic restrictions are too narrow
    and should be widened.
  correction: IPR008183 alone would annotate enzymes that are not galactose mutarotases. The Metazoa condition is
    what makes set 1 correct.
  error_type: CONJUNCTION_IGNORED
  evidence:
  - 'InterPro IPR008183 official name: Aldose 1-/Glucose-6-phosphate 1-epimerase (family)'
  - 'UniProtKB query xref:interpro-IPR008183 AND reviewed:true: 32 entries; with ec:5.1.3.3: 18; with ec:5.1.3.15:
    5 (2026-11-09)'
  - 'Same query restricted to taxonomy_id:33208 (Metazoa): 6 entries, 6 with ec:5.1.3.3'
  - Q03161 (S. cerevisiae YMR099C) glucose-6-phosphate 1-epimerase EC 5.1.3.15; P32139 (E. coli yihR) sulfoquinovose
    mutarotase EC 5.1.3.43
- date: '2026-11-10'
  withdrawn_claim: The FunFam being contained in IPR008183, and IPR008183 in IPR011013, makes the rule redundant.
  correction: The FunFam is in a separate, alternative condition set, so its containment in IPR008183 is not redundancy
    inside a conjunction. Only IPR011013 in set 1 is non-restrictive.
  error_type: CONJUNCTION_IGNORED
  evidence:
  - 'Live rule (rest.uniprot.org/arba/ARBA00001712, 2026-11-09): CS1 = IPR008183 AND IPR011013 AND Metazoa; CS2
    = FunFam 2.70.98.10:FF:000003 AND Eukaryota'
- date: '2026-11-10'
  withdrawn_claim: The rule covers only a small number of proteins (3029 unreviewed), suggesting poor sensitivity.
  correction: A protein count is not a sensitivity estimate, and limited coverage is not an error in the annotations
    the rule does make.
  error_type: LOW_RECALL_IS_NOT_WRONG
  evidence:
  - 'Live rule statistics: 0 reviewed, 2727 unreviewed proteins'
- date: '2026-11-10'
  withdrawn_claim: The rule is deficient because it provides no GO annotation.
  correction: The rule assigns a catalytic activity with a Rhea reaction and EC number. The absence of a second
    annotation type is not a defect of the rule.
  error_type: OTHER
  evidence:
  - 'Live rule annotation: CATALYTIC ACTIVITY, RHEA:28675, EC 5.1.3.3'