ARBA00022777

id: ARBA00022777
description: >-
  Assigns the UniProt keyword KW-0418 (Kinase) through 1,392 alternative condition sets built from InterPro,
  PANTHER and CATH FunFam signatures.
status: IN_PROGRESS
rule_type: ARBA
rule:
  rule_id: ARBA00022777
  condition_sets:
  - number: 1
    conditions:
    - condition_type: INTERPRO
      value: IPR006204
      curie: InterPro:IPR006204
      label: GHMP kinase N-terminal domain
      interpro_type: DOMAIN
      negated: false
    - condition_type: INTERPRO
      value: IPR020568
      curie: InterPro:IPR020568
      label: Ribosomal protein uS5 domain 2-type superfamily
      interpro_type: HOMOLOGOUS_SUPERFAMILY
      negated: false
    - condition_type: TAXON
      value: Bacteria
      curie: NCBITaxon:2
      label: Bacteria
      negated: false
    notes: >-
      Swiss-Prot entries matching the whole conjunction: 1022; of these 1022 carry KW-0418 Kinase (UniProtKB
      query, 2026-11-10). Examples with the keyword: P0A6T3 (galK), Q9XDM4 (pduX).
  - number: 2
    conditions:
    - condition_type: INTERPRO
      value: IPR000850
      curie: InterPro:IPR000850
      label: Adenylate kinase/UMP-CMP kinase
      interpro_type: FAMILY
      negated: false
    - condition_type: INTERPRO
      value: IPR027417
      curie: InterPro:IPR027417
      label: P-loop containing nucleoside triphosphate hydrolase
      interpro_type: HOMOLOGOUS_SUPERFAMILY
      negated: false
    - condition_type: INTERPRO
      value: IPR033690
      curie: InterPro:IPR033690
      label: Adenylate kinase, conserved site
      interpro_type: CONSERVED_SITE
      negated: false
    notes: >-
      Swiss-Prot entries matching the whole conjunction: 835; of these 835 carry KW-0418 Kinase (UniProtKB
      query, 2026-11-10). Examples with the keyword: P27144 (AK4), Q9UIJ7 (AK3).
  - number: 3
    conditions:
    - condition_type: INTERPRO
      value: IPR001048
      curie: InterPro:IPR001048
      label: Aspartate/glutamate/uridylate kinase
      interpro_type: DOMAIN
      negated: false
    - condition_type: INTERPRO
      value: IPR001057
      curie: InterPro:IPR001057
      label: Glutamate/acetylglutamate kinase
      interpro_type: FAMILY
      negated: false
    - condition_type: INTERPRO
      value: IPR036393
      curie: InterPro:IPR036393
      label: Acetylglutamate kinase-like superfamily
      interpro_type: HOMOLOGOUS_SUPERFAMILY
      negated: false
    notes: >-
      Swiss-Prot entries matching the whole conjunction: 767; of these 767 carry KW-0418 Kinase (UniProtKB
      query, 2026-11-10). Examples with the keyword: P54886 (ALDH18A1), O04226 (P5CS1).
  - number: 4
    conditions:
    - condition_type: INTERPRO
      value: IPR001576
      curie: InterPro:IPR001576
      label: Phosphoglycerate kinase
      interpro_type: FAMILY
      negated: false
    - condition_type: INTERPRO
      value: IPR015824
      curie: InterPro:IPR015824
      label: Phosphoglycerate kinase, N-terminal
      interpro_type: HOMOLOGOUS_SUPERFAMILY
      negated: false
    - condition_type: INTERPRO
      value: IPR036043
      curie: InterPro:IPR036043
      label: Phosphoglycerate kinase superfamily
      interpro_type: HOMOLOGOUS_SUPERFAMILY
      negated: false
    notes: >-
      Swiss-Prot entries matching the whole conjunction: 720; of these 720 carry KW-0418 Kinase (UniProtKB
      query, 2026-11-10). Examples with the keyword: P00558 (PGK1), P07205 (PGK2).
  - number: 5
    conditions:
    - condition_type: INTERPRO
      value: IPR008271
      curie: InterPro:IPR008271
      label: Serine/threonine-protein kinase, active site
      interpro_type: ACTIVE_SITE
      negated: false
    - condition_type: INTERPRO
      value: IPR017441
      curie: InterPro:IPR017441
      label: Protein kinase, ATP binding site
      interpro_type: BINDING_SITE
      negated: false
    - condition_type: TAXON
      value: Viridiplantae
      curie: NCBITaxon:33090
      label: Viridiplantae
      negated: false
    notes: >-
      Swiss-Prot entries matching the whole conjunction: 719; of these 719 carry KW-0418 Kinase (UniProtKB
      query, 2026-11-10). Examples with the keyword: A8R7E6 (CERK1), C0LGF4 (FEI1).
  - number: 6
    conditions:
    - condition_type: INTERPRO
      value: IPR006259
      curie: InterPro:IPR006259
      label: Adenylate kinase subfamily
      interpro_type: FAMILY
      negated: false
    notes: >-
      Swiss-Prot entries matching the whole conjunction: 701; of these 701 carry KW-0418 Kinase (UniProtKB
      query, 2026-11-10). Examples with the keyword: P27144 (AK4), Q9UIJ7 (AK3).
  - number: 7
    conditions:
    - condition_type: INTERPRO
      value: IPR018094
      curie: InterPro:IPR018094
      label: Thymidylate kinase
      interpro_type: FAMILY
      negated: false
    - condition_type: INTERPRO
      value: IPR039430
      curie: InterPro:IPR039430
      label: Thymidylate kinase-like domain
      interpro_type: DOMAIN
      negated: false
    - condition_type: PANTHER
      value: PTHR10344
      curie: PANTHER:PTHR10344
      label: THYMIDYLATE KINASE
      negated: false
    notes: >-
      Swiss-Prot entries matching the whole conjunction: 612; of these 612 carry KW-0418 Kinase (UniProtKB
      query, 2026-11-10). Examples with the keyword: P23919 (DTYMK), P00572 (CDC8).
  - number: 8
    conditions:
    - condition_type: INTERPRO
      value: IPR004662
      curie: InterPro:IPR004662
      label: Acetylglutamate kinase family
      interpro_type: FAMILY
      negated: false
    - condition_type: PANTHER
      value: PTHR23342
      curie: PANTHER:PTHR23342
      label: N-ACETYLGLUTAMATE SYNTHASE
      negated: false
    notes: >-
      Swiss-Prot entries matching the whole conjunction: 595; of these 595 carry KW-0418 Kinase (UniProtKB
      query, 2026-11-10). Examples with the keyword: Q01217 (ARG5,6), Q9SCL7 (NAGK).
  - number: 9
    conditions:
    - condition_type: INTERPRO
      value: IPR014721
      curie: InterPro:IPR014721
      label: Small ribosomal subunit protein uS5 domain 2-type fold, subgroup
      interpro_type: HOMOLOGOUS_SUPERFAMILY
      negated: false
    - condition_type: PANTHER
      value: PTHR43527
      curie: PANTHER:PTHR43527
      label: 4-DIPHOSPHOCYTIDYL-2-C-METHYL-D-ERYTHRITOL KINASE, CHLOROPLASTIC
      negated: false
    notes: >-
      Swiss-Prot entries matching the whole conjunction: 589; of these 589 carry KW-0418 Kinase (UniProtKB
      query, 2026-11-10). Examples with the keyword: Q9XDM4 (pduX), O81014 (ISPE).
  - number: 10
    conditions:
    - condition_type: INTERPRO
      value: IPR011994
      curie: InterPro:IPR011994
      label: Cytidylate kinase domain
      interpro_type: DOMAIN
      negated: false
    notes: >-
      Swiss-Prot entries matching the whole conjunction: 566; of these 566 carry KW-0418 Kinase (UniProtKB
      query, 2026-11-10). Examples with the keyword: P0A6I0 (cmk), P9WPA9 (cmk).
  go_annotations: []
  entries: []
  reviewed_protein_count: 0
  unreviewed_protein_count: 3762398
  created_date: '2020-05-12'
  modified_date: '2026-07-18'
  source_condition_set_count: 1392
  retrieved_date: '2026-11-09'
review_summary: >-
  All 1,392 live condition sets were screened with two UniProtKB queries each (2026-11-10): the Swiss-Prot
  entries that match the whole conjunction, and how many of them carry KW-0418 Kinase. Every screened
  set matches at least one Swiss-Prot entry. Summed over the screened sets there are 46,549 set-level
  matches (an entry that matches several sets is counted once per set) and 46,549 of them carry the keyword.
  No screened set has a Swiss-Prot match without the keyword. 10 sets are recorded in the rule block with
  official signature names; the other screened sets were checked by count only and their signatures were
  not read. 171 of the 1,392 sets have a taxon condition. ARBA rules are mined from Swiss-Prot annotation,
  so this screen shows that no screened set conflicts with curated keywords; it does not measure precision
  on the 3,762,398 unreviewed entries the rule annotates.
action: UNDECIDED
action_rationale: >-
  The rule was not read set by set: 10 of 1,392 condition sets are recorded and 1,392 were screened by
  count. Nothing found argues against the rule. The keyword Kinase is defined by UniProt as: Enzyme that
  catalyzes the transfer of phosphate (phosphoryl or pyrophosphoryl transfer) usually from ATP to a second
  substrate. It is a class label, so diversity among its members is expected, and in every screened set
  all Swiss-Prot matches carry it. UniProt maps KW-0418 to GO:0016301 kinase activity. A verdict on the
  whole rule needs every set to be read and precision on unreviewed entries to be measured.
annotation_assessments:
- annotation_kind: KEYWORD
  value: KW-0418
  label: Kinase
  assessment: UNDECIDED
  correct_examples:
  - P0A6T3
  - Q9XDM4
  - P27144
  - Q9UIJ7
  - P54886
  - O04226
  - P00558
  - P07205
  notes: >-
    UniProt keyword KW-0418 definition: Enzyme that catalyzes the transfer of phosphate (phosphoryl or
    pyrophosphoryl transfer) usually from ATP to a second substrate. UniProt keyword-to-GO mapping: GO:0016301
    kinase activity. Set-level Swiss-Prot matches in the screened sets 46,549; with the keyword 46,549.
    The examples are Swiss-Prot entries that match a recorded condition set and carry the keyword.
corrections:
- date: '2026-11-10'
  withdrawn_claim: >-
    The rule will annotate ATP-binding proteins, pseudokinases, helicases and chaperones as kinases.
  correction: No such protein was named and none was found among reviewed matches.
  error_type: UNEXAMINED_RULE
  evidence:
  - 'Previous version: condition_sets []'
  - >-
    All 46,549 set-level Swiss-Prot matches of the 1,392 live sets carry KW-0418 (UniProtKB, 2026-11-10)
- date: '2026-11-10'
  withdrawn_claim: >-
    1,358 condition sets and 462 InterPro domains make the rule unsuitable; it should be removed.
  correction: The number of condition sets is not evidence about correctness.
  error_type: SIZE_AS_EVIDENCE
  evidence:
  - >-
    Live rule: 1,392 condition sets; every set has Swiss-Prot matches and all of them carry the keyword
- date: '2026-11-10'
  withdrawn_claim: The keyword Kinase gives no functional information and conflates distinct kinase classes.
  correction: >-
    It is a class label that is true of all of them; UniProt maps it to a GO molecular function term.
  error_type: GENERAL_IS_NOT_WRONG
  evidence:
  - >-
    UniProt KW-0418 definition: Enzyme that catalyzes the transfer of phosphate (phosphoryl or pyrophosphoryl
    transfer) usually from ATP to a second substrate.
  - 'UniProt keyword KW-0418 geneOntologies: GO:0016301 kinase activity'
- date: '2026-11-10'
  withdrawn_claim: Literature contradicts the rule because kinome studies classify kinases into families.
  correction: >-
    A finer classification does not contradict the superclass label, and the only source cited was the
    rule's own manual note.
  error_type: UNSUPPORTED_SOURCE
  evidence:
  - >-
    All previous supported_by entries cited rules/arba/ARBA00022777/ARBA00022777-deep-research-manual.md
- date: '2026-11-10'
  withdrawn_claim: The rule ignores taxonomy by covering bacteria, archaea, eukaryotes and viruses.
  correction: Kinases occur in all of these, and part of the rule is taxon-restricted.
  error_type: TAXON_MISREAD
  evidence:
  - 171 of the 1,392 live condition sets have a taxon condition
- date: '2026-11-10'
  withdrawn_claim: The recommended action was REMOVE.
  correction: >-
    REMOVE is not an action for a rule review, and the grounds given do not support retiring the rule.
  error_type: OTHER
  evidence:
  - 'RuleActionEnum: ACCEPT, MODIFY, DEPRECATE, SPLIT, MERGE, UNDECIDED'