# Curated Pfam entry review (entry-centric; see src/ai_gene_review/schema/pfam_entry_review.yaml).
# Sidecar to the machine-fetched PF13360-metadata.yaml (do not hand-edit metadata).
# Hand-curated; examples/counter-examples verified against UniProt (reviewed entries).
pfam_id: PF13360
pfam_name: PQQ_2
pfam_description: PQQ/WD40-like beta-propeller repeat domain; named for BamB but a fold shared across functions.
interpro:
  id: InterPro:IPR002372
  label: PQQ_rpt_dom
  type: Domain
  member_pfams:
  - id: Pfam:PF13360
    label: PQQ_2
    is_subject: true
    note: beta-propeller repeat domain found in BamB but also in kinases and dehydrogenases
  - id: Pfam:PF01011
    label: PQQ
    note: PQQ beta-propeller (quinoprotein dehydrogenases)
  - id: Pfam:PF13570
    label: Beta-prop_ACSF4
    note: beta-propeller repeat domain
  go_status: ABSENT
  mapping_viability: NOT_VIABLE
  viability_reason: >-
    InterPro:IPR002372 is a beta-propeller repeat fold shared by catalytic
    quinoproteins and other propellers, so a process-specific term cannot sit on it.
proposed_annotations:
- term:
    id: GO:0043165
    label: Gram-negative-bacterium-type cell outer membrane assembly
  relation:
    id: RO:0002331
    label: involved in
  aspect: biological_process
  confidence: LOW
  status: REJECTED
  rationale: >-
    REJECTED on member verification. The outer-membrane assembly factor BamB
    (UniProt:P77774) is a member, but reviewed PF13360 membership also includes
    protein kinases (RqkA, AfsK; EC 2.7.11.1) and a quinoprotein alcohol dehydrogenase
    (PedH; EC 1.1.2.-). PF13360 is a beta-propeller fold module, not a BamB-specific
    signature, so an OM-assembly term would over-annotate even at the Pfam level.
  supporting_examples:
  - accession: UniProt:P77774
    protein_name: BAMB_ECOLI (outer membrane protein assembly factor BamB)
    organism: Escherichia coli K12
    reviewed: true
    note: The eponymous member; a genuine BAM-complex accessory lipoprotein.
  counter_examples:
  - accession: UniProt:Q9RRH3
    protein_name: RQKA_DEIRA (DNA-damage-responsive Ser/Thr protein kinase RqkA)
    organism: Deinococcus radiodurans
    member_pfam: Pfam:PF13360
    ec: 2.7.11.1
    reviewed: true
    reason: Same family (PF13360) but a protein kinase, no role in OM assembly; proves the family is heterogeneous.
  - accession: UniProt:Q88JH0
    protein_name: PEDH_PSEPK (quinoprotein alcohol dehydrogenase PedH)
    organism: Pseudomonas putida KT2440
    member_pfam: Pfam:PF13360
    ec: 1.1.2.-
    reviewed: true
    gene_review: genes/PSEPK/pedH/pedH-ai-review.yaml
    reason: Same family but a periplasmic alcohol dehydrogenase (reviewed in this repo); an OM-assembly term would mis-annotate it.
notes: >-
  Cautionary case: the beta-propeller fold is reused across BamB, signaling kinases and
  dehydrogenases. We have an in-repo review for one of the counter-examples (PedH).