id: D3VIU4
gene_symbol: D3VIU4
taxon:
  id: NCBITaxon:406817
  label: Xenorhabdus nematophila
status: COMPLETE
description: >-
  The signal peptide and soluble solute-binding domain are incompatible with intrinsic ligand-gated channel
  activity.
source_documents:
  - genes/XENNA/D3VIU4/D3VIU4-uniprot.txt
  - genes/XENNA/D3VIU4/D3VIU4-goa.tsv
  - genes/XENNA/D3VIU4/D3VIU4-hypotheses/prediction-ligand-gated-ion-channel/openscientist.md
predictions:
  - source_method: ProtNLM2
    source_version: UniProt 2024_06 pilot
    predicted_term:
      id: GO:0015276
      label: ligand-gated monoatomic ion channel activity
    predicted_term_type: GO_MF
    review:
      assessment: NPI
      error_type: DOMAIN_ARCHITECTURE_MISMATCH
      confidence_score: 0
      summary: >-
        The 262-residue target has an N-terminal signal peptide followed by a solute-binding protein family
        3 domain covering residues 40–259. This is the architecture of an exported ligand-binding component,
        without a membrane-spanning channel pore after signal-peptide removal. Binding a transported ligand
        does not make the binding component a ligand-gated ion channel. The predicted intrinsic channel
        activity is absent from the cached annotations and is contradicted by the available architecture.
      supported_by:
        - reference_id: file:XENNA/D3VIU4/D3VIU4-uniprot.txt
          supporting_text: >-
            ID   D3VIU4_XENNA            Unreviewed;       262 AA. ... DR   InterPro; IPR018313; SBP_3_CS.
            ... DR   InterPro; IPR001638; Solute-binding_3/MltF_N. ... FT   SIGNAL          1..28 ...
            FT   DOMAIN          40..259 ... FT                   /note="Solute-binding protein family
            3/N-terminal"
        - reference_id: file:XENNA/D3VIU4/D3VIU4-hypotheses/prediction-ligand-gated-ion-channel/openscientist.md
          supporting_text: >-
            D3VIU4 has the binding clamshell but **none of the channel/pore module**
references:
  - id: file:XENNA/D3VIU4/D3VIU4-uniprot.txt
    title: D3VIU4-uniprot.txt
  - id: file:XENNA/D3VIU4/D3VIU4-hypotheses/prediction-ligand-gated-ion-channel/openscientist.md
    title: openscientist.md