id: Q9US48
gene_symbol: gaa1
taxon:
  id: NCBITaxon:284812
  label: "Schizosaccharomyces pombe 972h-"
status: DRAFT
description: 'BioReason-Pro RL web export for gaa1 (SCHPO). GO-GPT produced 61 non-root terms; 16 non-generic IS_A leaf terms
  retained (MF:1 BP:12 CC:3). Deterministic exact comparison against current AIGR: CNN:2 NPI:1 UNC:13. Remaining UNC entries
  require manual assessment. [ONTOLOGY_LABEL_AUDIT] The raw export contained 13 ID/label pairs that differ from current GO
  labels; structured leaf labels were normalized and the raw source was retained.'
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-hypotheses/prediction-cysteine-endopeptidase/openscientist.md
  title: OpenScientist review of the gaa1 cysteine-type endopeptidase prediction
source_documents:
- genes/SCHPO/gaa1/gaa1-bioreason-rl-predictions.md
- genes/SCHPO/gaa1/gaa1-hypotheses/prediction-cysteine-endopeptidase/openscientist.md
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: >-
      Refuted on independent OpenScientist review. GO:0004197 is not present in
      GOA for gaa1, so this would be a novel incorrect molecular-function
      addition. The catalytic cysteine-protease activity of the GPI transamidase
      complex maps to the Gpi8/PIG-K subunit, which carries the Peptidase_C13
      domain and active-site residues; gaa1 is a distinct GPI-T subunit with no
      cysteine-protease domain, no annotated catalytic residues, and no EC number.
      Any possible Gaa1/GPAA1 contribution to amide-bond formation would be
      mechanistically incompatible with cysteine-type endopeptidase activity.
    supported_by:
    - reference_id: file:SCHPO/gaa1/gaa1-hypotheses/prediction-cysteine-endopeptidase/openscientist.md
      supporting_text: The prediction is REFUTED.
    - 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
- 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:1901576
    label: obsolete organic substance biosynthetic process
  predicted_term_type: GO_BP
  review:
    assessment: UNC
    confidence_score: 1
    summary: No deterministic exact-action match resolves this prediction in the current AIGR review. Requires manual assessment.
      [ONTOLOGY_LABEL_AUDIT] Raw BioReason label 'organic substance biosynthetic process' did not match the current GO label
      'obsolete organic substance biosynthetic process'; the structured label was normalized from GO and the raw source was
      retained.
- 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:1901564
    label: obsolete organonitrogen compound metabolic process
  predicted_term_type: GO_BP
  review:
    assessment: UNC
    confidence_score: 1
    summary: No deterministic exact-action match resolves this prediction in the current AIGR review. Requires manual assessment.
      [ONTOLOGY_LABEL_AUDIT] Raw BioReason label 'organonitrogen compound metabolic process' did not match the current GO
      label 'obsolete organonitrogen compound metabolic process'; the structured label was normalized from GO and the raw
      source was retained.
- 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:0044255
    label: obsolete cellular lipid metabolic process
  predicted_term_type: GO_BP
  review:
    assessment: UNC
    confidence_score: 1
    summary: No deterministic exact-action match resolves this prediction in the current AIGR review. Requires manual assessment.
      [ONTOLOGY_LABEL_AUDIT] Raw BioReason label 'cellular lipid metabolic process' did not match the current GO label 'obsolete
      cellular lipid metabolic process'; the structured label was normalized from GO and the raw source was retained.
- 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:0044249
    label: obsolete cellular biosynthetic process
  predicted_term_type: GO_BP
  review:
    assessment: UNC
    confidence_score: 1
    summary: No deterministic exact-action match resolves this prediction in the current AIGR review. Requires manual assessment.
      [ONTOLOGY_LABEL_AUDIT] Raw BioReason label 'cellular biosynthetic process' did not match the current GO label 'obsolete
      cellular biosynthetic process'; the structured label was normalized from GO and the raw source was retained.
- 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:1901566
    label: obsolete organonitrogen compound biosynthetic process
  predicted_term_type: GO_BP
  review:
    assessment: UNC
    confidence_score: 1
    summary: No deterministic exact-action match resolves this prediction in the current AIGR review. Requires manual assessment.
      [ONTOLOGY_LABEL_AUDIT] Raw BioReason label 'organonitrogen compound biosynthetic process' did not match the current
      GO label 'obsolete organonitrogen compound biosynthetic process'; the structured label was normalized from GO and the
      raw source was retained.
- 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:0006643
    label: obsolete membrane lipid metabolic process
  predicted_term_type: GO_BP
  review:
    assessment: UNC
    confidence_score: 1
    summary: No deterministic exact-action match resolves this prediction in the current AIGR review. Requires manual assessment.
      [ONTOLOGY_LABEL_AUDIT] Raw BioReason label 'membrane lipid metabolic process' did not match the current GO label 'obsolete
      membrane lipid metabolic process'; the structured label was normalized from GO and the raw source was retained.
- 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:0034645
    label: obsolete cellular macromolecule biosynthetic process
  predicted_term_type: GO_BP
  review:
    assessment: UNC
    confidence_score: 1
    summary: No deterministic exact-action match resolves this prediction in the current AIGR review. Requires manual assessment.
      [ONTOLOGY_LABEL_AUDIT] Raw BioReason label 'cellular macromolecule biosynthetic process' did not match the current GO
      label 'obsolete cellular macromolecule biosynthetic process'; the structured label was normalized from GO and the raw
      source was retained.
- 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:0046467
    label: obsolete membrane lipid biosynthetic process
  predicted_term_type: GO_BP
  review:
    assessment: UNC
    confidence_score: 1
    summary: No deterministic exact-action match resolves this prediction in the current AIGR review. Requires manual assessment.
      [ONTOLOGY_LABEL_AUDIT] Raw BioReason label 'membrane lipid biosynthetic process' did not match the current GO label
      'obsolete membrane lipid biosynthetic process'; the structured label was normalized from GO and the raw source was retained.
- 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:0042158
    label: lipoprotein biosynthetic process
  predicted_term_type: GO_BP
  review:
    assessment: UNC
    confidence_score: 1
    summary: No deterministic exact-action match resolves this prediction in the current AIGR review. Requires manual assessment.
- 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:0006497
    label: protein lipidation
  predicted_term_type: GO_BP
  review:
    assessment: UNC
    confidence_score: 1
    summary: No deterministic exact-action match resolves this prediction in the current AIGR review. Requires manual assessment.
- 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:0006506
    label: GPI anchor biosynthetic process
  predicted_term_type: GO_BP
  review:
    assessment: CNN
    confidence_score: 2
    summary: 'Deterministic exact-match comparison: current AIGR action(s) KEEP_AS_NON_CORE retain this GO term, so it is
      correct but not novel.'
- 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:0006661
    label: phosphatidylinositol biosynthetic process
  predicted_term_type: GO_BP
  review:
    assessment: UNC
    confidence_score: 1
    summary: No deterministic exact-action match resolves this prediction in the current AIGR review. Requires manual assessment.
- 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:0005737
    label: cytoplasm
  predicted_term_type: GO_CC
  review:
    assessment: UNC
    confidence_score: 1
    summary: No deterministic exact-action match resolves this prediction in the current AIGR review. Requires manual assessment.
- 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:0012505
    label: endomembrane system
  predicted_term_type: GO_CC
  review:
    assessment: UNC
    confidence_score: 1
    summary: No deterministic exact-action match resolves this prediction in the current AIGR review. Requires manual assessment.
- 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:0005783
    label: endoplasmic reticulum
  predicted_term_type: GO_CC
  review:
    assessment: CNN
    confidence_score: 2
    summary: 'Deterministic exact-match comparison: current AIGR action(s) KEEP_AS_NON_CORE retain this GO term, so it is
      correct but not novel.'