ARBA00027651 phosphoprotein phosphatase activity (GO:0004721)

id: ARBA00027651
description: Assigns GO:0004721 phosphoprotein phosphatase activity through 82 alternative condition sets
  of InterPro, PANTHER and CATH FunFam signatures, half with a taxon condition.
status: IN_PROGRESS
rule_type: ARBA
rule:
  rule_id: ARBA00027651
  condition_sets:
  - number: 1
    conditions:
    - condition_type: INTERPRO
      value: IPR000242
      curie: InterPro:IPR000242
      label: Tyrosine-specific protein phosphatase, PTPase domain
      interpro_type: DOMAIN
      negated: false
    - condition_type: INTERPRO
      value: IPR003961
      curie: InterPro:IPR003961
      label: Fibronectin type III
      interpro_type: DOMAIN
      negated: false
    - condition_type: INTERPRO
      value: IPR050348
      curie: InterPro:IPR050348
      label: Protein-Tyrosine Phosphatase
      interpro_type: FAMILY
      negated: false
    notes: 'UniProtKB query, November 2026: 16 Swiss-Prot and 8379 TrEMBL entries match. QuickGO, GO:0004721
      or a descendant on the Swiss-Prot entries: 11 with experimental evidence, 3 with other manual evidence
      only, 2 with IEA only, 0 with none. Examples: P08575 (PTPRC_HUMAN) GO:0004725 protein tyrosine phosphatase
      activity, IDA, PMID:2853967; Q15262 (PTPRK_HUMAN) GO:0004725 protein tyrosine phosphatase activity,
      IDA, PMID:16263724; P23470 (PTPRG_HUMAN) GO:0004725 protein tyrosine phosphatase activity, IDA,
      PMID:19167335. No bacterial or archaeal entry matches this conjunction (0 of 8,395 UniProtKB matches).'
  go_annotations:
  - go_id: GO:0004721
    go_label: phosphoprotein phosphatase activity
    aspect: MF
  entries: []
  reviewed_protein_count: 0
  unreviewed_protein_count: 0
  created_date: '2021-10-20'
  modified_date: '2026-07-18'
  retrieved_date: '2026-11-09'
  source_condition_set_count: 82
review_summary: One of the 82 live condition sets was examined (set 1, receptor-type protein tyrosine
  phosphatases). Its Swiss-Prot matches are experimentally annotated to GO:0004725 protein tyrosine phosphatase
  activity, a child of the rule's term, and the set matches no prokaryotic protein. No wrongly annotated
  protein has been identified. The review is open.
action: UNDECIDED
action_rationale: The rule was not examined set by set. The one set checked is supported. That GO:0004721
  is the parent of the tyrosine, serine/threonine and dual-specificity terms makes it general, not wrong.
annotation_assessments:
- annotation_kind: GO_TERM
  value: GO:0004721
  label: phosphoprotein phosphatase activity
  assessment: UNDECIDED
  correct_examples:
  - P08575
  - Q15262
  - P23470
  - P23471
  - B9EKR1
  - P16620
  - H2KZM6
  - P04157
  - Q62656
  - P06800
  - P35832
  notes: Set 1 receipts are in rule.condition_sets[0].notes; listed accessions have experimental evidence
    for a descendant of GO:0004721 (QuickGO). The other 81 sets were not examined.
corrections:
- date: '2026-11-10'
  withdrawn_claim: The rule applies eukaryotic receptor PTP families to prokaryotes, where they do not
    exist.
  correction: The receptor-PTP set has no taxon condition but matches no prokaryotic protein.
  error_type: TAXON_MISREAD
  evidence:
  - 'UniProtKB query (xref:interpro-IPR000242) AND (xref:interpro-IPR003961) AND (xref:interpro-IPR050348):
    8,395 entries'
  - 'Same query AND ((taxonomy_id:2) OR (taxonomy_id:2157)): 0 entries'
- date: '2026-11-10'
  withdrawn_claim: GO:0004721 is too general; the rule should be deprecated and replaced by rules for
    GO:0004725, GO:0004722 and GO:0008138.
  correction: All three proposed terms are children of GO:0004721, so the rule's annotation is true for
    those proteins. A true general term is not grounds for removal.
  error_type: GENERAL_IS_NOT_WRONG
  evidence:
  - 'QuickGO: ancestors of GO:0004725, GO:0004722 and GO:0008138 each include GO:0004721'
- date: '2026-11-10'
  withdrawn_claim: There is a high risk of false positives from promiscuous structural domains.
  correction: No domain and no wrongly annotated protein was named.
  error_type: UNEXAMINED_RULE
  evidence:
  - 'Old review: rule.condition_sets empty, no accession cited'
- date: '2026-11-10'
  withdrawn_claim: 74 condition sets exceed the limit of 12 and cannot be analysed.
  correction: The limit of 12 is the default of this repository's overlap-analysis tool. The number of
    alternative sets is not evidence that any of them is wrong.
  error_type: SIZE_AS_EVIDENCE
  evidence:
  - 'src/ai_gene_review/etl/rule_analysis.py: max_condition_sets: int = 12 (default of the overlap-analysis
    tool)'