ProtNLM2 External predictions
View prediction review YAML · WDPCP-protnlm-predictions-review.yaml · Review status: COMPLETE
Broad ciliary and cytoskeletal roles are supported by mammalian experiments and the conserved horse scaffold.
Source documents: projects/PROTNLM_EVALUATION/mammal-benchmark/horse40-predictions.csv · projects/PROTNLM_EVALUATION/mammal-benchmark/predictions.jsonl.gz · projects/PROTNLM_EVALUATION/mammal-benchmark/paired-sequences/WDPCP.json · genes/HORSE/WDPCP/WDPCP-hypotheses/horse40-cell-projection-organization/openscientist.md
Review score: 2 = concordant with evidence; 1 = uncertain; 0 = discordant with evidence. This is an assessment score, not a model probability.
COR — Correct novel prediction Review score: 2/2
Prediction method: ProtNLM2 · Version: UniProt API snapshot 2026-09-08
Review rationale: Wdpcp loss disrupts cilia and actin-based protrusive behavior. Conservation of the WD40/alpha-solenoid scaffold supports the broad cell-projection-organization prediction; the OpenScientist 83% identity estimate and cached 88.1% identity over 704 paired residues reflect different alignment scopes but the same WDPCP orthology. The N-terminal length difference resembles known human–mouse variation; a short lipid-binding-tail deletion leaves affinity, not this entire broad role, unresolved. More specific children such as cilium assembly and establishment of planar polarity are better supported, and any horse assignment should use ISS/ISO rather than experimental evidence.
Supporting Evidence:
- PMID:24302887: "Wdpcp is localized to the transition zone"
- PMID:24302887: "decreased membrane ruffling, failure to establish cell polarity, and loss of directional cell migration."
- file:HORSE/WDPCP/WDPCP-bioinformatics/RESULTS.md: "share 88.1% identity among 704 paired residues."
- PMID:35427153: "Compared to mouse, the human Wdpcp has an N-terminal extension of ~35 residues that is not resolved in the map."
- file:HORSE/WDPCP/WDPCP-bioinformatics/RESULTS.md: "The WD40/alpha-solenoid scaffold is extensively conserved, supporting broad ciliary and cytoskeletal roles."
- file:HORSE/WDPCP/WDPCP-hypotheses/horse40-cell-projection-organization/openscientist.md: "GO:0030030 is therefore biologically justified for the horse protein. The two curation caveats are that the term is generic (specific children such as cilium assembly and establishment of planar polarity are better supported) and that all functional evidence is transferred by orthology to an unreviewed TrEMBL record, so an **ISS/ISO** evidence code is appropriate rather than an experimental one."
COR — Correct novel prediction Review score: 2/2
Prediction method: ProtNLM2 · Version: UniProt API snapshot 2026-09-08
Review rationale: Mouse imaging directly detects a cytoplasmic WDPCP pool on actin and focal adhesions. The conserved horse architecture supports this localization independently of electronic annotation agreement.
Supporting Evidence:
- PMID:24302887: "Wdpcp is also found in the cytoplasm, where it is localized in the actin cytoskeleton and in focal adhesions."
- file:HORSE/WDPCP/WDPCP-bioinformatics/RESULTS.md: "share 88.1% identity among 704 paired residues."
- file:HORSE/WDPCP/WDPCP-bioinformatics/RESULTS.md: "The WD40/alpha-solenoid scaffold is extensively conserved, supporting broad ciliary and cytoskeletal roles."
COR — Correct novel prediction Review score: 2/2
Prediction method: ProtNLM2 · Version: UniProt API snapshot 2026-09-08
Review rationale: Transition-zone localization places WDPCP at the ciliary base. Conserved horse scaffold architecture supports this broad cilium location; it does not establish axonemal shaft localization.
Supporting Evidence:
- PMID:24302887: "Wdpcp is localized to the transition zone"
- file:HORSE/WDPCP/WDPCP-bioinformatics/RESULTS.md: "share 88.1% identity among 704 paired residues."
- file:HORSE/WDPCP/WDPCP-bioinformatics/RESULTS.md: "The WD40/alpha-solenoid scaffold is extensively conserved, supporting broad ciliary and cytoskeletal roles."
COR — Correct novel prediction Review score: 2/2
Prediction method: ProtNLM2 · Version: UniProt API snapshot 2026-09-08
Review rationale: Wdpcp localizes to the actin cytoskeleton and recruits Sept2. The conserved horse scaffold supports a cytoskeletal pool, without requiring it to be an actin motor or a tubulin polymerization enzyme.
Supporting Evidence:
- PMID:24302887: "Wdpcp is also found in the cytoplasm, where it is localized in the actin cytoskeleton and in focal adhesions."
- PMID:24302887: "in Wdpcp-deficient cells, Sept2 was lost from the actin cytoskeleton, suggesting Wdpcp is required for Sept2 recruitment to actin filaments."
- file:HORSE/WDPCP/WDPCP-bioinformatics/RESULTS.md: "share 88.1% identity among 704 paired residues."
- file:HORSE/WDPCP/WDPCP-bioinformatics/RESULTS.md: "The WD40/alpha-solenoid scaffold is extensively conserved, supporting broad ciliary and cytoskeletal roles."