# Curated Pfam entry review (entry-centric; see src/ai_gene_review/schema/pfam_entry_review.yaml).
# Sidecar to the machine-fetched PF02431-metadata.yaml (do not hand-edit metadata).
# Hand-curated; examples/counter-examples verified against UniProt (reviewed entries).
pfam_id: PF02431
pfam_name: Chalcone
pfam_description: Chalcone-flavanone isomerase (CHI), the catalytic family of the chalcone-isomerase clan.
interpro:
  id: InterPro:IPR016087
  label: Chalcone_isomerase
  type: Domain
  member_pfams:
  - id: Pfam:PF02431
    label: Chalcone
    is_subject: true
    note: catalytic chalcone-flavanone isomerase (CHI)
  - id: Pfam:PF16035
    label: Chalcone_2
    note: chalcone-isomerase-like (CHIL); includes non-catalytic fatty-acid-binding members
  - id: Pfam:PF16036
    label: Chalcone_3
    note: chalcone-isomerase-like (CHIL)
  go_status: ABSENT
  mapping_viability: NOT_VIABLE
  viability_reason: >-
    The entry lumps catalytic CHI (PF02431) with chalcone-isomerase-like (CHIL) families
    (PF16035/PF16036) whose characterized members are non-catalytic fatty-acid-binding
    proteins. A chalcone isomerase term on the whole entry would over-annotate the CHIL
    members, so the term belongs at the PF02431 level only.
proposed_annotations:
- term:
    id: GO:0045430
    label: chalcone isomerase activity
  relation:
    id: RO:0002327
    label: enables
  aspect: molecular_function
  confidence: HIGH
  status: PROPOSED
  rationale: >-
    Reviewed members of PF02431 are experimentally characterized chalcone-flavanone
    isomerases (EC 5.5.1.6) across multiple plant lineages, and the catalytic CHI fold
    is the defining feature of this family (vs the non-catalytic CHIL siblings). The
    family-function alignment is strong, not just nominal.
  supporting_examples:
  - accession: UniProt:P41088
    protein_name: CFI1_ARATH (chalcone--flavanone isomerase 1 / TT5)
    organism: Arabidopsis thaliana
    ec: 5.5.1.6
    reviewed: true
  - accession: UniProt:P28012
    protein_name: CFI1_MEDSA (chalcone--flavanone isomerase 1)
    organism: Medicago sativa
    ec: 5.5.1.6
    reviewed: true
  - accession: UniProt:A2IBF8
    protein_name: CFI_GOSHI (chalcone--flavanone isomerase)
    organism: Gossypium hirsutum
    ec: 5.5.1.6
    reviewed: true
  counter_examples:
  - accession: UniProt:Q9M1X2
    protein_name: FAP1_ARATH (fatty-acid-binding protein 1; CHI-family protein 1)
    organism: Arabidopsis thaliana
    member_pfam: Pfam:PF16035
    reviewed: true
    reason: CHIL-family member with no isomerase activity (no EC); binds fatty acids. Would be wrongly annotated if the term sat on the InterPro entry.
  - accession: UniProt:Q84RK2
    protein_name: FAP2_ARATH (fatty-acid-binding protein 2; CHI-family protein 2)
    organism: Arabidopsis thaliana
    member_pfam: Pfam:PF16035
    reviewed: true
    reason: Non-catalytic CHIL protein (no EC); demonstrates the entry is functionally heterogeneous.
notes: >-
  PF02431 is the catalytic CHI family of the Chalcone-like clan; the sibling CHIL
  families are the reason the term cannot live on InterPro:IPR016087.