ARBA00004841

id: ARBA00004841
description: Assigns the pathway comment "Glycan metabolism; heparin biosynthesis" to chordate proteins that carry
  both the sulfotransferase domain (IPR000863) and the heparan sulphate N-deacetylase domain (IPR021930), or CATH
  FunFam 3.40.50.300:FF:000176. Both sets identify the bifunctional heparan sulfate N-deacetylase/N-sulfotransferases
  (NDST1-4).
status: COMPLETE
rule_type: ARBA
rule:
  rule_id: ARBA00004841
  condition_sets:
  - number: 1
    conditions:
    - condition_type: INTERPRO
      value: IPR000863
      curie: InterPro:IPR000863
      label: Sulfotransferase domain
      interpro_type: DOMAIN
      negated: false
    - condition_type: INTERPRO
      value: IPR021930
      curie: InterPro:IPR021930
      label: Heparan sulphate-N-deacetylase, deacetylase domain
      interpro_type: DOMAIN
      negated: false
    - condition_type: TAXON
      value: Chordata
      curie: NCBITaxon:7711
      label: Chordata
      negated: false
    notes: 'Swiss-Prot entries matching this set (2026-11-09): 12. 12 carry the PATHWAY comment "Glycan metabolism;
      heparin biosynthesis". UniProtKB entries matching: 4029.'
  - number: 2
    conditions:
    - condition_type: FUNFAM
      value: 3.40.50.300:FF:000176
      curie: CATH.FunFam:3.40.50.300:FF:000176
      label: bifunctional heparan sulfate N-deacetylase/N-sulfotransferase 1
      negated: false
    - condition_type: TAXON
      value: Chordata
      curie: NCBITaxon:7711
      label: Chordata
      negated: false
    notes: 'Swiss-Prot entries matching this set (2026-11-09): 12. 12 carry the PATHWAY comment "Glycan metabolism;
      heparin biosynthesis". UniProtKB entries matching: 3386.'
  go_annotations: []
  entries: []
  reviewed_protein_count: 0
  unreviewed_protein_count: 4061
  created_date: '2020-05-12'
  modified_date: '2026-07-18'
  retrieved_date: '2026-11-09'
  source_condition_set_count: 2
review_summary: Both live condition sets were checked against Swiss-Prot. Each matches 12 reviewed entries, all
  NDST family members (e.g. human P52848 NDST1, P52849 NDST2, O95803 NDST3, Q9H3R1 NDST4), and all 12 carry the
  pathway comment. 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: 12 of 12 Swiss-Prot matches of each set carry the pathway
  comment the rule assigns.'
taxonomic_scope:
  assessment: APPROPRIATE
  notes: Both sets are restricted to Chordata, and all 12 Swiss-Prot matches of each set carry the pathway comment.
annotation_assessments:
- annotation_kind: OTHER
  value: 'PATHWAY: Glycan metabolism; heparin biosynthesis'
  assessment: CORRECT
  correct_examples:
  - P52848
  - P52849
  - O95803
  - Q9H3R1
  - O97583
  - P52850
  notes: 'Set 1: 12 Swiss-Prot matches, 12 with the pathway comment. Set 2: 12 Swiss-Prot matches, 12 with the pathway
    comment. UniProtKB matches: 4029 (set 1) and 3386 (set 2); rule statistics report 4061 unreviewed proteins.'
confidence: 0.8
corrections:
- date: '2026-11-10'
  withdrawn_claim: Condition set 1 includes the broad P-loop superfamily IPR027417 (40,360 Swiss-Prot proteins),
    which creates substantial false positive risk; it should be removed to eliminate false positives from unrelated
    ATP-binding proteins.
  correction: 'IPR027417 was one conjunct of an AND. A broad conjunct cannot widen a conjunction: the set matched
    only proteins that also had IPR021930. The live rule no longer contains IPR027417.'
  error_type: CONJUNCTION_IGNORED
  evidence:
  - 'Overlap data recorded in the earlier version of this file: Swiss-Prot IPR021930 = 15, all 15 inside IPR000863
    (152), all 152 inside IPR027417 (40,360)'
  - Live rule (2026-11-09) CS1 = IPR000863 AND IPR021930 AND Chordata
  - 'Swiss-Prot matches of live CS1: 12, of which 12 carry the pathway comment'
- date: '2026-11-10'
  withdrawn_claim: GO:0008467 (N-acetylglucosaminyltransferase activity) and GO:0015020 (glucuronosyltransferase
    activity) should be added.
  correction: GO:0008467 is [heparan sulfate]-glucosamine 3-sulfotransferase activity, not an N-acetylglucosaminyltransferase
    term, and neither it nor GO:0015020 describes NDST. The N-sulfotransferase reaction of NDST is GO:0015016.
  error_type: WRONG_IDENTIFIER_MEANING
  evidence:
  - 'QuickGO GO:0008467: [heparan sulfate]-glucosamine 3-sulfotransferase activity'
  - 'QuickGO GO:0015020: glucuronosyltransferase activity (UDP-glucuronate + acceptor)'
  - 'QuickGO GO:0015016: heparan sulfate N-sulfotransferase activity'
- date: '2026-11-10'
  withdrawn_claim: The rule has three condition sets, including a glucuronyl C5-epimerase set (IPR010598, IPR039721,
    IPR059154) with redundant domains, and a Eukaryota restriction.
  correction: The live rule has two condition sets, both restricted to Chordata, and no C5-epimerase set.
  error_type: STALE_RULE_VERSION
  evidence:
  - 'rest.uniprot.org/arba/ARBA00004841 retrieved 2026-11-09: 2 condition sets, modifiedDate as recorded in rule.modified_date'
- date: '2026-11-10'
  withdrawn_claim: The rule needs significant modification because it provides only a pathway annotation without
    GO terms.
  correction: The rule is a pathway-comment rule and the comment it assigns is correct for every reviewed match.
    Not emitting GO terms is not an error.
  error_type: OTHER
  evidence:
  - 'Live rule annotation: commentType PATHWAY, "Glycan metabolism; heparin biosynthesis"'