ARBA00022825

id: ARBA00022825
description: >-
  Assigns the UniProt keyword Serine protease (KW-0720) through 244 alternative condition sets, each
  one to three InterPro entries or PANTHER families, in part with a taxon.
status: IN_PROGRESS
rule_type: ARBA
rule:
  rule_id: ARBA00022825
  condition_sets:
  - number: 1
    conditions:
    - condition_type: INTERPRO
      value: IPR001907
      curie: InterPro:IPR001907
      label: ATP-dependent Clp protease proteolytic subunit
      negated: false
    - condition_type: INTERPRO
      value: IPR023562
      curie: InterPro:IPR023562
      label: Clp protease proteolytic subunit /Translocation-enhancing protein TepA
      negated: false
    - condition_type: INTERPRO
      value: IPR033135
      curie: InterPro:IPR033135
      label: ClpP, histidine active site
      negated: false
    notes: >-
      UniProtKB release 2026_04: 703 reviewed entries match this set; 703 of them carry keyword KW-0720.
      30331 unreviewed entries match.
  - number: 2
    conditions:
    - condition_type: INTERPRO
      value: IPR018215
      curie: InterPro:IPR018215
      label: ClpP, Ser active site
      negated: false
    - condition_type: INTERPRO
      value: IPR029045
      curie: InterPro:IPR029045
      label: ClpP/crotonase-like domain superfamily
      negated: false
    notes: >-
      UniProtKB release 2026_04: 625 reviewed entries match this set; 625 of them carry keyword KW-0720.
      21284 unreviewed entries match.
  - number: 3
    conditions:
    - condition_type: PANTHER
      value: PTHR10381:SF70
      curie: PANTHER:PTHR10381:SF70
      label: ATP-DEPENDENT CLP PROTEASE PROTEOLYTIC SUBUNIT
      negated: false
    notes: >-
      UniProtKB release 2026_04: 589 reviewed entries match this set; 589 of them carry keyword KW-0720.
      26153 unreviewed entries match.
  - number: 4
    conditions:
    - condition_type: INTERPRO
      value: IPR000209
      curie: InterPro:IPR000209
      label: Peptidase S8/S53 domain
      negated: false
    - condition_type: INTERPRO
      value: IPR015500
      curie: InterPro:IPR015500
      label: Peptidase S8, subtilisin-related
      negated: false
    - condition_type: INTERPRO
      value: IPR036852
      curie: InterPro:IPR036852
      label: Peptidase S8/S53 domain superfamily
      negated: false
    notes: >-
      UniProtKB release 2026_04: 368 reviewed entries match this set; 368 of them carry keyword KW-0720.
      126302 unreviewed entries match.
  - number: 5
    conditions:
    - condition_type: INTERPRO
      value: IPR023828
      curie: InterPro:IPR023828
      label: Peptidase S8, subtilisin, Ser-active site
      negated: false
    notes: >-
      UniProtKB release 2026_04: 338 reviewed entries match this set; 338 of them carry keyword KW-0720.
      115914 unreviewed entries match.
  - number: 6
    conditions:
    - condition_type: INTERPRO
      value: IPR003593
      curie: InterPro:IPR003593
      label: AAA+ ATPase domain
      negated: false
    - condition_type: INTERPRO
      value: IPR008269
      curie: InterPro:IPR008269
      label: Peptidase S16, Lon proteolytic domain
      negated: false
    - condition_type: INTERPRO
      value: IPR027065
      curie: InterPro:IPR027065
      label: Lon protease
      negated: false
    notes: >-
      UniProtKB release 2026_04: 199 reviewed entries match this set; 199 of them carry keyword KW-0720.
      26337 unreviewed entries match.
  - number: 7
    conditions:
    - condition_type: INTERPRO
      value: IPR018114
      curie: InterPro:IPR018114
      label: Serine protease-like, trypsin family, histidine active site
      negated: false
    - condition_type: INTERPRO
      value: IPR033116
      curie: InterPro:IPR033116
      label: Serine proteases, trypsin family, serine active site
      negated: false
    - condition_type: PANTHER
      value: PTHR24271
      curie: PANTHER:PTHR24271
      label: KALLIKREIN-RELATED
      negated: false
    notes: >-
      UniProtKB release 2026_04: 195 reviewed entries match this set; 195 of them carry keyword KW-0720.
      7575 unreviewed entries match.
  - number: 8
    conditions:
    - condition_type: INTERPRO
      value: IPR050131
      curie: InterPro:IPR050131
      label: Subtilisin-like serine protease
      negated: false
    - condition_type: TAXON
      value: Eukaryota
      curie: NCBITaxon:2759
      label: Eukaryota
      negated: false
    notes: >-
      UniProtKB release 2026_04: 182 reviewed entries match this set; 182 of them carry keyword KW-0720.
      24164 unreviewed entries match.
  - number: 9
    conditions:
    - condition_type: INTERPRO
      value: IPR008268
      curie: InterPro:IPR008268
      label: Peptidase S16, active site
      negated: false
    notes: >-
      UniProtKB release 2026_04: 167 reviewed entries match this set; 167 of them carry keyword KW-0720.
      22375 unreviewed entries match.
  - number: 10
    conditions:
    - condition_type: INTERPRO
      value: IPR034193
      curie: InterPro:IPR034193
      label: Proteinase K-like catalytic domain
      negated: false
    notes: >-
      UniProtKB release 2026_04: 167 reviewed entries match this set; 167 of them carry keyword KW-0720.
      14821 unreviewed entries match.
  go_annotations: []
  entries: []
  reviewed_protein_count: 0
  unreviewed_protein_count: 511900
  created_date: '2020-05-12'
  modified_date: '2026-07-18'
  retrieved_date: '2026-11-09'
  source_condition_set_count: 244
review_summary: >-
  The first 10 of the 244 live condition sets were examined. They select ClpP, subtilisin (peptidase
  S8), Lon, kallikrein-related trypsin-family and proteinase K-like families, and every reviewed match
  carries the Serine protease keyword (3533 of 3533, summed over sets). The other 234 sets were not
  examined.
action: UNDECIDED
action_rationale: >-
  The rule was sampled, not examined set by set, so no verdict is given. The sampled sets are sound,
  which removes the grounds of the earlier verdict but does not establish that every set is right.
  The counts are from Swiss-Prot, which is also what ARBA learns its rules from, so they show the
  condition sets are coherent rather than giving an independent error rate for unreviewed entries.
annotation_assessments:
- annotation_kind: KEYWORD
  value: KW-0720
  label: Serine protease
  assessment: UNDECIDED
  correct_examples:
  - Q16740
  - P0A6G7
  - P29120
  notes: >-
    UniProtKB release 2026_04, reviewed entries matching a set and carrying KW-0720: set 1, Q16740
    (human CLPP) and P0A6G7 (Escherichia coli clpP); set 4, P29120 (human PCSK1). Per-set counts are
    in the condition set notes.
corrections:
- date: '2026-11-10'
  withdrawn_claim: >-
    The rule probably captures many non-protease proteins and has a high false positive risk, because
    its domain collection is too broad.
  correction: >-
    The condition sets had not been read when this was written, and no falsely annotated protein was
    named. In the ten sets examined every reviewed match carries the keyword.
  error_type: UNEXAMINED_RULE
  evidence:
  - The old file recorded condition_sets as an empty list.
  - 'UniProtKB release 2026_04: per-set counts for sets 1 to 10 are in the condition set notes.'
- date: '2026-11-10'
  withdrawn_claim: 240 condition sets indicate poor curation, and the sets are probably redundant.
  correction: >-
    The number of sets is not evidence about accuracy. Overlap between alternative sets cannot produce
    a wrong or conflicting annotation, since the rule has one consequent.
  error_type: SIZE_AS_EVIDENCE
  evidence:
  - 'UniProt ARBA API, ARBA00022825, retrieved 2026-11-09: 244 condition sets, one annotation.'
- date: '2026-11-10'
  withdrawn_claim: The rule should be removed because it gives no GO term.
  correction: The consequent is a UniProt keyword by design.
  error_type: OTHER
  evidence:
  - 'UniProt ARBA API, ARBA00022825: single annotation, keyword KW-0720 Serine protease.'
- date: '2026-11-10'
  withdrawn_claim: >-
    The rule has not been validated against reviewed entries, as its reviewed protein count is 0.
  correction: >-
    The zero is the statistic the ARBA API reports for the rule, not a validation result. Reviewed
    entries do match the condition sets.
  error_type: OTHER
  evidence:
  - 'UniProtKB release 2026_04: set 1 matches 703 reviewed entries, set 4 matches 368.'
- date: '2026-11-10'
  withdrawn_claim: Taxonomic scope is missing because some sets have taxon restrictions and others
    do not.
  correction: >-
    Each set is a separate alternative; a taxon condition on one set and none on another is not an
    inconsistency.
  error_type: TAXON_MISREAD
  evidence:
  - 'UniProt ARBA API, ARBA00022825: 96 of 244 condition sets contain a taxon condition.'