id: Q9W288
gene_symbol: NtR
taxon:
  id: NCBITaxon:7227
  label: Drosophila melanogaster
status: COMPLETE
description: The generic ligand-gated channel prediction is supported by Cys-loop channel architecture,
  while ligand identity, calcium permeability and cholinergic signaling remain unresolved.
source_documents:
- projects/PROTNLM_EVALUATION/fly-benchmark/predictions.jsonl.gz
- genes/DROME/NtR/NtR-predictions-source.json
- genes/DROME/NtR/NtR-hypotheses/ntr-cholinergic-calcium-and-synaptic-functions/openscientist.md
references:
- id: file:DROME/NtR/NtR-family-evidence.md
  title: DROME/NtR/NtR-family-evidence.md
  findings: []
- id: file:DROME/NtR/NtR-flybase.txt
  title: DROME/NtR/NtR-flybase.txt
  findings: []
- id: PMID:30429615
  title: Improved reference genome of Aedes aegypti informs arbovirus vector control.
  full_text_unavailable: false
  findings: []
- id: file:DROME/NtR/NtR-hypotheses/ntr-cholinergic-calcium-and-synaptic-functions/openscientist.md
  title: OpenScientist audit of NtR cholinergic, calcium and synaptic functions
  findings:
  - statement: OpenScientist found general Cys-loop ligand-gated ion-channel annotations defensible
      while leaving acetylcholine identity, calcium permeability and synaptic function unestablished.
    supporting_text: At a **general** level, terms describing it as a **ligand-gated / cation-permeable
      ion channel of the Cys-loop family localized to the plasma membrane** are defensible.
predictions:
- source_method: ProtNLM2
  source_version: UniProt API snapshot 2026-09-08
  predicted_term:
    id: GO:0005230
    label: extracellular ligand-gated monoatomic ion channel activity
  predicted_term_type: GO_MF
  review:
    assessment: CNN
    confidence_score: 2
    summary: The generic ligand-gated channel claim is supported by the published Cys-loop channel-family
      tree, which includes Dmel NTR, and the target ligand-binding/channel architecture. It already appears
      in the exact-accession GOA record. NtR lies outside the identified nicotinic receptor groups, so
      this broad result does not validate the narrower acetylcholine-gating or calcium-permeability annotations.
      The OpenScientist audit reached the same split, retaining broad channel terms and downscoping
      the acetylcholine, calcium and cholinergic assignments as untested computational propagation.
    supported_by:
    - reference_id: file:DROME/NtR/NtR-family-evidence.md
      supporting_text: The published Cys-loop ligand-gated ion-channel tree in Matthews et al. (2018),
        Extended Data Figure 10d, includes Dmel NTR as a distinct branch outside both shaded nicotinic
        acetylcholine-receptor groups.
    - reference_id: file:DROME/NtR/NtR-flybase.txt
      supporting_text: UNCLASSIFIED LIGAND-GATED ION CHANNEL SUBUNITS
    - reference_id: PMID:30429615
      supporting_text: Many insecticides act on ion channels, and we curated members of the Cys-loop ligand-gated
        ion channel (Cys-loop LGIC) superfamily in AaegL5.
    - reference_id: file:DROME/NtR/NtR-hypotheses/ntr-cholinergic-calcium-and-synaptic-functions/openscientist.md
      supporting_text: 'NtR is a *bona fide* member of the Cys-loop ligand-gated ion channel (LGIC) superfamily:
        it has a *bona fide* extracellular neurotransmitter-gated ion-channel ligand-binding domain
        (Pfam PF02931), one canonical Cys-loop signature (C337–x13–C351), and a four-transmembrane-helix
        C-terminal region (M1–M4) in the expected Cys-loop topology'