# Curated Pfam entry review (entry-centric; see src/ai_gene_review/schema/pfam_entry_review.yaml).
# Sidecar to the machine-fetched PF07228-metadata.yaml (do not hand-edit metadata).
# Hand-curated; examples/counter-examples verified against UniProt (reviewed entries).
pfam_id: PF07228
pfam_name: SpoIIE
pfam_description: Stage II sporulation protein E (SpoIIE), the sporulation-specific PP2C-family phosphatase.
interpro:
  id: InterPro:IPR001932
  label: PPM-type_phosphatase-like_dom
  type: Domain
  member_pfams:
  - id: Pfam:PF07228
    label: SpoIIE
    is_subject: true
    note: SpoIIE sporulation phosphatase
  - id: Pfam:PF00481
    label: PP2C
    note: generic PP2C-type protein phosphatase domain (not sporulation-specific)
  - id: Pfam:PF13672
    label: PP2C_2
    note: generic PP2C-type protein phosphatase domain
  go_status: ABSENT
  mapping_viability: NOT_VIABLE
  viability_reason: >-
    The PP2C phosphatase fold (PF00481/PF13672) is shared across thousands of
    substrate-diverse protein phosphatases. The molecular function (phosphatase) is
    common to the whole entry, but the biological process "sporulation" is specific to
    the SpoIIE family, so the sporulation term belongs at PF07228, not on the entry.
proposed_annotations:
- term:
    id: GO:0030435
    label: sporulation resulting in formation of a cellular spore
  relation:
    id: RO:0002331
    label: involved in
  aspect: biological_process
  confidence: HIGH
  status: PROPOSED
  rationale: >-
    SpoIIE is the Stage II sporulation protein E phosphatase that activates sigma-F
    during Bacillus endospore formation; its sporulation role is the defining feature
    of the family. The proposed term is already curated on a SwissProt-reviewed member
    that we have independently reviewed in this repo (see supporting_examples).
  supporting_examples:
  - accession: UniProt:P37475
    protein_name: SP2E_BACSU (stage II sporulation protein E)
    organism: Bacillus subtilis
    reviewed: true
    gene_review: genes/BACSU/spoIIE/spoIIE-ai-review.yaml
    note: reviewed in this repo; the GOA + our review carry GO:0030435.
  counter_examples:
  - accession: UniProt:O15297
    protein_name: PPM1D_HUMAN (protein phosphatase 1D / PP2C-delta)
    organism: Homo sapiens
    member_pfam: Pfam:PF00481
    ec: 3.1.3.16
    reviewed: true
    reason: Generic PP2C phosphatase with no role in sporulation; shares only the phosphatase fold.
  - accession: UniProt:P49593
    protein_name: PPM1F_HUMAN (protein phosphatase 1F / CaMKP)
    organism: Homo sapiens
    member_pfam: Pfam:PF00481
    ec: 3.1.3.16
    reviewed: true
    reason: CaMK phosphatase, unrelated to sporulation; would be mis-annotated by an entry-level sporulation term.
notes: >-
  The MF (protein-serine/threonine phosphatase) is genuinely shared by the InterPro
  entry; only the BP (sporulation) is SpoIIE-specific, which is why this review proposes
  the BP term at the Pfam level rather than the MF.