ARBA00022679

id: ARBA00022679
description: >-
  Assigns the UniProt keyword KW-0808 (Transferase) through 4,603 alternative condition sets built from
  InterPro, PANTHER and CATH FunFam signatures.
status: IN_PROGRESS
rule_type: ARBA
rule:
  rule_id: ARBA00022679
  condition_sets:
  - number: 1
    conditions:
    - condition_type: INTERPRO
      value: IPR001986
      curie: InterPro:IPR001986
      label: Enolpyruvate transferase domain
      interpro_type: DOMAIN
      negated: false
    - condition_type: INTERPRO
      value: IPR013792
      curie: InterPro:IPR013792
      label: RNA 3'-terminal phosphate cyclase/enolpyruvate transferase, alpha/beta
      interpro_type: HOMOLOGOUS_SUPERFAMILY
      negated: false
    - condition_type: INTERPRO
      value: IPR036968
      curie: InterPro:IPR036968
      label: Enolpyruvate transferase domain superfamily
      interpro_type: HOMOLOGOUS_SUPERFAMILY
      negated: false
    notes: >-
      Swiss-Prot entries matching the whole conjunction: 1218; of these 1218 carry KW-0808 Transferase
      (UniProtKB query, 2026-11-10). Examples with the keyword: P0A6D3 (aroA), P08566 (ARO1).
  - number: 11
    conditions:
    - condition_type: INTERPRO
      value: IPR044893
      curie: InterPro:IPR044893
      label: RNA polymerase Rpb1, clamp domain superfamily
      interpro_type: HOMOLOGOUS_SUPERFAMILY
      negated: false
    notes: >-
      Swiss-Prot entries matching the whole conjunction: 913; of these 913 carry KW-0808 Transferase (UniProtKB
      query, 2026-11-10). Examples with the keyword: P24928 (POLR2A), O14802 (POLR3A).
  - number: 21
    conditions:
    - condition_type: INTERPRO
      value: IPR043502
      curie: InterPro:IPR043502
      label: DNA/RNA polymerase superfamily
      interpro_type: HOMOLOGOUS_SUPERFAMILY
      negated: false
    - condition_type: TAXON
      value: Riboviria
      curie: NCBITaxon:2559587
      label: Riboviria
      negated: false
    notes: >-
      Swiss-Prot entries matching the whole conjunction: 802; of these 802 carry KW-0808 Transferase (UniProtKB
      query, 2026-11-10). Examples with the keyword: A2I7M2 (no gene name), A3FMB2 (no gene name).
  - number: 31
    conditions:
    - condition_type: INTERPRO
      value: IPR001737
      curie: InterPro:IPR001737
      label: Ribosomal RNA adenine methyltransferase KsgA/Erm
      interpro_type: FAMILY
      negated: false
    - condition_type: INTERPRO
      value: IPR029063
      curie: InterPro:IPR029063
      label: S-adenosyl-L-methionine-dependent methyltransferase superfamily
      interpro_type: HOMOLOGOUS_SUPERFAMILY
      negated: false
    notes: >-
      Swiss-Prot entries matching the whole conjunction: 726; of these 726 carry KW-0808 Transferase (UniProtKB
      query, 2026-11-10). Examples with the keyword: Q8WVM0 (TFB1M), Q9H5Q4 (TFB2M).
  - number: 41
    conditions:
    - condition_type: INTERPRO
      value: IPR004383
      curie: InterPro:IPR004383
      label: Ribosomal RNA large subunit methyltransferase RlmN/Cfr
      interpro_type: FAMILY
      negated: false
    - condition_type: INTERPRO
      value: IPR013785
      curie: InterPro:IPR013785
      label: Aldolase-type TIM barrel
      interpro_type: HOMOLOGOUS_SUPERFAMILY
      negated: false
    - condition_type: INTERPRO
      value: IPR040072
      curie: InterPro:IPR040072
      label: Methyltransferase (Class A)
      interpro_type: FAMILY
      negated: false
    notes: >-
      Swiss-Prot entries matching the whole conjunction: 669; of these 669 carry KW-0808 Transferase (UniProtKB
      query, 2026-11-10). Examples with the keyword: P36979 (rlmN), O34617 (rlmN).
  - number: 51
    conditions:
    - condition_type: INTERPRO
      value: IPR050065
      curie: InterPro:IPR050065
      label: Bifunctional protein GlmU-like
      interpro_type: FAMILY
      negated: false
    notes: >-
      Swiss-Prot entries matching the whole conjunction: 617; of these 617 carry KW-0808 Transferase (UniProtKB
      query, 2026-11-10). Examples with the keyword: P0ACC7 (glmU), Q97R46 (glmU).
  - number: 61
    conditions:
    - condition_type: INTERPRO
      value: IPR016064
      curie: InterPro:IPR016064
      label: NAD kinase/diacylglycerol kinase-like domain superfamily
      interpro_type: HOMOLOGOUS_SUPERFAMILY
      negated: false
    - condition_type: INTERPRO
      value: IPR017437
      curie: InterPro:IPR017437
      label: ATP-NAD kinase, PpnK-type, C-terminal
      interpro_type: HOMOLOGOUS_SUPERFAMILY
      negated: false
    - condition_type: INTERPRO
      value: IPR017438
      curie: InterPro:IPR017438
      label: Inorganic polyphosphate/ATP-NAD kinase, N-terminal
      interpro_type: HOMOLOGOUS_SUPERFAMILY
      negated: false
    notes: >-
      Swiss-Prot entries matching the whole conjunction: 547; of these 547 carry KW-0808 Transferase (UniProtKB
      query, 2026-11-10). Examples with the keyword: Q4G0N4 (NADK2), O95544 (NADK).
  - number: 71
    conditions:
    - condition_type: INTERPRO
      value: IPR010280
      curie: InterPro:IPR010280
      label: (Uracil-5)-methyltransferase family
      interpro_type: FAMILY
      negated: false
    - condition_type: INTERPRO
      value: IPR030390
      curie: InterPro:IPR030390
      label: RNA methyltransferase TrmA, active site
      interpro_type: ACTIVE_SITE
      negated: false
    notes: >-
      Swiss-Prot entries matching the whole conjunction: 528; of these 528 carry KW-0808 Transferase (UniProtKB
      query, 2026-11-10). Examples with the keyword: P23003 (trmA), P33753 (TRM2).
  - number: 81
    conditions:
    - condition_type: INTERPRO
      value: IPR000860
      curie: InterPro:IPR000860
      label: Porphobilinogen deaminase
      interpro_type: FAMILY
      negated: false
    - condition_type: INTERPRO
      value: IPR022417
      curie: InterPro:IPR022417
      label: Porphobilinogen deaminase, N-terminal
      interpro_type: DOMAIN
      negated: false
    - condition_type: PANTHER
      value: PTHR11557:SF0
      curie: PANTHER:PTHR11557:SF0
      label: PORPHOBILINOGEN DEAMINASE
      negated: false
    notes: >-
      Swiss-Prot entries matching the whole conjunction: 477; of these 477 carry KW-0808 Transferase (UniProtKB
      query, 2026-11-10). Examples with the keyword: P08397 (HMBS), P06983 (hemC).
  - number: 91
    conditions:
    - condition_type: INTERPRO
      value: IPR000891
      curie: InterPro:IPR000891
      label: Pyruvate carboxyltransferase
      interpro_type: DOMAIN
      negated: false
    - condition_type: INTERPRO
      value: IPR002034
      curie: InterPro:IPR002034
      label: Alpha-isopropylmalate/homocitrate synthase, conserved site
      interpro_type: CONSERVED_SITE
      negated: false
    notes: >-
      Swiss-Prot entries matching the whole conjunction: 453; of these 453 carry KW-0808 Transferase (UniProtKB
      query, 2026-11-10). Examples with the keyword: Q9FN52 (MAM3), P06208 (LEU4).
  go_annotations: []
  entries: []
  reviewed_protein_count: 0
  unreviewed_protein_count: 12487598
  created_date: '2020-05-12'
  modified_date: '2026-07-18'
  source_condition_set_count: 4603
  retrieved_date: '2026-11-09'
review_summary: >-
  461 of the 4,603 live condition sets (every tenth set, starting with set 1) 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-0808 Transferase. Every screened set matches at least one Swiss-Prot entry. Summed over
  the screened sets there are 21,413 set-level matches (an entry that matches several sets is counted
  once per set) and 21,413 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. 385 of the 4,603 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 12,487,598 unreviewed entries the rule annotates.
action: UNDECIDED
action_rationale: >-
  The rule was not read set by set: 10 of 4,603 condition sets are recorded and 461 were screened by count.
  Nothing found argues against the rule. The keyword Transferase is defined by UniProt as: Enzyme that
  transfers a chemical group, e.g. a methyl group or a glycosyl group from one compound (donor) to another
  compound (acceptor). 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-0808 to GO:0016740 transferase 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-0808
  label: Transferase
  assessment: UNDECIDED
  correct_examples:
  - P0A6D3
  - P08566
  - P24928
  - O14802
  - A2I7M2
  - A3FMB2
  - Q8WVM0
  - Q9H5Q4
  notes: >-
    UniProt keyword KW-0808 definition: Enzyme that transfers a chemical group, e.g. a methyl group or
    a glycosyl group from one compound (donor) to another compound (acceptor). UniProt keyword-to-GO mapping:
    GO:0016740 transferase activity. Set-level Swiss-Prot matches in the screened sets 21,413; with the
    keyword 21,413. The examples are Swiss-Prot entries that match a recorded condition set and carry
    the keyword.
corrections:
- date: '2026-11-10'
  withdrawn_claim: Condition set 1 is IPR001986, Fumarylacetoacetate hydrolase.
  correction: >-
    IPR001986 is the Enolpyruvate transferase domain, and set 1 is a conjunction of three InterPro entries.
  error_type: WRONG_IDENTIFIER_MEANING
  evidence:
  - 'InterPro IPR001986 name: Enolpyruvate transferase domain'
  - 'Live set 1: IPR001986 AND IPR013792 AND IPR036968'
- date: '2026-11-10'
  withdrawn_claim: The rule has no taxonomic restrictions.
  correction: Part of the rule is taxon-restricted.
  error_type: TAXON_MISREAD
  evidence:
  - 385 of the 4,603 live condition sets have a taxon condition
- date: '2026-11-10'
  withdrawn_claim: >-
    Applying one keyword to 14 million proteins through thousands of condition sets is over-annotation,
    and the rule should be removed.
  correction: Neither the number of proteins nor the number of sets is evidence about correctness.
  error_type: SIZE_AS_EVIDENCE
  evidence:
  - >-
    Live rule: 4,603 condition sets; in the 461 sets screened, all 21,413 set-level Swiss-Prot matches
    carry KW-0808 (UniProtKB, 2026-11-10)
- date: '2026-11-10'
  withdrawn_claim: >-
    The Transferase keyword is meaningless and conflates kinases, methyltransferases and other 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-0808 definition: Enzyme that transfers a chemical group, e.g. a methyl group or a glycosyl
    group from one compound (donor) to another compound (acceptor).
  - 'UniProt keyword KW-0808 geneOntologies: GO:0016740 transferase activity'
- date: '2026-11-10'
  withdrawn_claim: >-
    The rule covers phosphatases and histone deacetylases and likely creates more false positives than
    true annotations.
  correction: >-
    No condition set matching a phosphatase or deacetylase was identified and no false positive was shown.
  error_type: UNEXAMINED_RULE
  evidence:
  - Previous version recorded one condition set of 4,473 and no matched protein
  - No Swiss-Prot match of any of the 461 screened sets lacks the keyword
- date: '2026-11-10'
  withdrawn_claim: >-
    Literature contradicts the rule, on the evidence of GO annotation principles and the rule's own deep-research
    note.
  correction: >-
    A finer EC classification does not contradict the superclass label; the sources cited were not literature.
  error_type: UNSUPPORTED_SOURCE
  evidence:
  - >-
    Previous supported_by reference ids: GO_ANNOTATION_PRINCIPLES and rules/arba/ARBA00022679/ARBA00022679-deep-research-analysis.md