id: A0A9L0IIU3
gene_symbol: ATG4C
taxon:
  id: NCBITaxon:9793
  label: Equus asinus
status: COMPLETE
description: Assessment of 3 ProtNLM2 GO predictions for donkey ATG4C (A0A9L0IIU3), using the human Swiss-Prot
  record Q96DT6, cached ATG4 biochemistry papers, and a donkey-human comparison (94.98% identity, full length,
  catalytic Cys111/Asp345/His347 conserved). Protein delipidation is correct and absent from the donkey GOA
  record as a process (COR). Proteolysis and autophagy are correct but less precise than the protein processing,
  cysteine-type endopeptidase and autophagosome assembly annotations already present (LSP). ProtNLM2 emitted
  no non-GO function-text or subcellular-location output for this accession in the frozen snapshot.
source_documents:
- genes/EQUAS/ATG4C/ATG4C-uniprot.txt
- genes/EQUAS/ATG4C/ATG4C-goa.tsv
- genes/EQUAS/ATG4C/ATG4C-bioinformatics/human_Q96DT6-uniprot.txt
- genes/EQUAS/ATG4C/ATG4C-bioinformatics/RESULTS.md
- projects/PROTNLM_EVALUATION/donkey40/donkey40-predictions.tsv
predictions:
- source_method: ProtNLM2
  source_version: UniProt API snapshot 2026-10-14
  predicted_term:
    id: GO:0006508
    label: proteolysis
  predicted_term_type: GO_BP
  review:
    assessment: LSP
    confidence_score: 2
    summary: ATG4C is a C54-family cysteine protease that cleaves ATG8 proteins, and the donkey protein conserves
      the catalytic nucleophile. Proteolysis is therefore correct, but the donkey GOA record already carries
      protein processing (a child of proteolysis) and cysteine-type endopeptidase activity, so the prediction
      is less precise than existing annotations.
    supported_by:
    - reference_id: file:EQUAS/ATG4C/ATG4C-bioinformatics/human_Q96DT6-uniprot.txt
      supporting_text: 'FUNCTION: Cysteine protease that plays a key role in autophagy by'
    - reference_id: file:EQUAS/ATG4C/ATG4C-bioinformatics/RESULTS.md
      supporting_text: 'ACT_SITE (Nucleophile): human [111] C -> donkey [111] C.'
- source_method: ProtNLM2
  source_version: UniProt API snapshot 2026-10-14
  predicted_term:
    id: GO:0051697
    label: protein delipidation
  predicted_term_type: GO_BP
  review:
    assessment: COR
    confidence_score: 2
    summary: All four mammalian ATG4 paralogs delipidate membrane-anchored ATG8 proteins in reconstituted
      assays, and human ATG4C displays stronger delipidation than priming activity in the curated human UniProt function statement. The
      donkey protein is a full-length ortholog with the catalytic triad conserved. The donkey GOA record has
      the corresponding molecular function (protein-phosphatidylethanolamine deconjugating activity) but not
      this process term, so the prediction adds a correct, target-novel process annotation.
    supported_by:
    - reference_id: PMID:29458288
      supporting_text: all 4 ATG4 proteases can be activated to similar enzymatic activities on lipid-attached
        substrates
    - reference_id: file:EQUAS/ATG4C/ATG4C-bioinformatics/human_Q96DT6-uniprot.txt
      supporting_text: while it displays stronger delipidation activity (PubMed:29458288)
    - reference_id: file:EQUAS/ATG4C/ATG4C-bioinformatics/RESULTS.md
      supporting_text: The donkey sequence A0A9L0IIU3 (458 residues) aligns to human Q96DT6 (458 residues)
        with 94.98% identity across 458 paired residues.
- source_method: ProtNLM2
  source_version: UniProt API snapshot 2026-10-14
  predicted_term:
    id: GO:0006914
    label: autophagy
  predicted_term_type: GO_BP
  review:
    assessment: LSP
    confidence_score: 2
    summary: ATG4C acts in autophagy by priming and delipidating ATG8 proteins, so the term is correct. The
      donkey GOA record already has more specific autophagy annotations (autophagosome assembly, aggrephagy),
      so the prediction is less precise than existing annotations.
    supported_by:
    - reference_id: file:EQUAS/ATG4C/ATG4C-bioinformatics/human_Q96DT6-uniprot.txt
      supporting_text: 'FUNCTION: Cysteine protease that plays a key role in autophagy by'
    - reference_id: PMID:21177865
      supporting_text: a key step in autophagosome biogenesis
references:
- id: file:EQUAS/ATG4C/ATG4C-bioinformatics/human_Q96DT6-uniprot.txt
  title: UniProt Swiss-Prot record for human ATG4C (Q96DT6)
  findings: []
- id: file:EQUAS/ATG4C/ATG4C-bioinformatics/RESULTS.md
  title: 'ATG4C: donkey-human sequence comparison'
  findings: []
- id: PMID:29458288
  title: Delipidation of mammalian Atg8-family proteins by each of the four ATG4 proteases.
  findings: []
- id: PMID:21177865
  title: Kinetics comparisons of mammalian Atg4 homologues indicate selective preferences toward diverse Atg8
    substrates.
  findings: []