id: Q9US48
gene_symbol: gaa1
locus_tag: SPAC1002.11
taxon:
  id: NCBITaxon:284812
  label: "Schizosaccharomyces pombe 972h-"
status: COMPLETE
description: GO-GPT's cysteine-type endopeptidase activity prediction is a subunit-level transfer of
  Gpi8/PIG-K catalytic chemistry onto noncatalytic Gaa1.
source_documents:
- genes/SCHPO/gaa1/gaa1-gogpt-leaf-predictions.yaml
- genes/SCHPO/gaa1/gaa1-bioreason-rl-predictions.md
- genes/SCHPO/gaa1/gaa1-hypotheses/prediction-cysteine-endopeptidase/openscientist.md
references:
- id: doi:10.64898/2026.03.19.712954
  title: 'BioReason-Pro: Advancing Protein Function Prediction with Multimodal Biological Reasoning'
- id: file:SCHPO/gaa1/gaa1-gogpt-leaf-predictions.yaml
  title: GO-GPT leaf predictions for gaa1 from the BioReason-Pro RL export
  findings:
  - statement: GO-GPT predicted cysteine-type endopeptidase activity for S. pombe gaa1.
    supporting_text: 'label: cysteine-type endopeptidase activity'
    reference_section_type: RESULTS
- id: file:SCHPO/gaa1/gaa1-bioreason-rl-predictions.md
  title: BioReason-Pro RL prediction export for gaa1
  findings:
  - statement: The raw BioReason export included cysteine-type endopeptidase activity in its molecular-function
      prediction path for gaa1.
    supporting_text: cysteine-type endopeptidase activity (`GO:0004197`)
    reference_section_type: RESULTS
- id: file:SCHPO/gaa1/gaa1-hypotheses/prediction-cysteine-endopeptidase/openscientist.md
  title: OpenScientist focused report on the gaa1 cysteine-type endopeptidase prediction
  findings:
  - statement: The focused report refuted the cysteine-type endopeptidase prediction because the catalytic
      subunit is Gpi8/PIG-K, not Gaa1.
    supporting_text: the catalytic cysteine-protease/transamidase activity belongs to Gpi8/PIG-K.
    reference_section_type: RESULTS
  - statement: Adding GO:0004197 to gaa1 would be a novel incorrect molecular-function assignment rather
      than a correction of an existing row.
    supporting_text: the prediction would be a **new, incorrect molecular-function addition** rather
      than a correction of an existing annotation
    reference_section_type: RESULTS
  - statement: Gaa1 lacks a compatible cysteine-protease domain signature.
    supporting_text: GO:0004197 is contradicted at the domain level.
    reference_section_type: RESULTS
  reference_review:
    relevance: HIGH
    correctness: UNVERIFIED
    review_notes: Focused report directly addresses the GO-GPT GO:0004197 prediction and distinguishes
      noncatalytic Gaa1 from the Gpi8/PIG-K catalytic subunit of the GPI transamidase complex.
predictions:
- source_method: GO-GPT
  source_version: bioreason.net/2026-03/rl
  source_reference_id: doi:10.64898/2026.03.19.712954
  predicted_term:
    id: GO:0004197
    label: cysteine-type endopeptidase activity
  predicted_term_type: GO_MF
  review:
    assessment: NPI
    confidence_score: 0
    error_type: COMPLEX_ACTIVITY_TRANSFER
    summary: Gaa1 is a noncatalytic GPI-transamidase subunit. The cysteine-protease/transamidase active
      site resides in Gpi8/PIG-K, while Gaa1 contributes substrate/lipid recognition and complex positioning.
      GO:0004197 would therefore be a new subunit-level misassignment.
    supported_by:
    - reference_id: file:SCHPO/gaa1/gaa1-gogpt-leaf-predictions.yaml
      supporting_text: 'label: cysteine-type endopeptidase activity'
    - reference_id: file:SCHPO/gaa1/gaa1-hypotheses/prediction-cysteine-endopeptidase/openscientist.md
      supporting_text: the catalytic cysteine-protease/transamidase activity belongs to Gpi8/PIG-K.
    - reference_id: file:SCHPO/gaa1/gaa1-hypotheses/prediction-cysteine-endopeptidase/openscientist.md
      supporting_text: GO:0004197 is contradicted at the domain level.