ProtNLM2 External predictions
View prediction review YAML · PPP4R4-protnlm-predictions-review.yaml · Review status: COMPLETE
Phosphatase regulation and complex membership are supported by conserved PP4R4 biology; blastocyst hatching remains unverified.
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/PPP4R4.json
Review score: 2 = concordant with evidence; 1 = uncertain; 0 = discordant with evidence. This is an assessment score, not a model probability.
UNC — Uncertain Review score: 1/2
Prediction method: ProtNLM2 · Version: UniProt API snapshot 2026-09-08
Review rationale: The primary human PP4R4 study establishes a cytosolic PP4 complex and altered phosphatase activity, not an embryonic hatching function. A nearly full-length horse homolog supports transfer of the molecular complex role but does not by itself establish this specific developmental process. Gene-specific embryo evidence or a traced functional mechanism is needed; absence of such evidence is not proof that the process is impossible.
Supporting Evidence:
- PMID:18715871: "we identify a novel, stable cytosolic PP4c interacting partner, KIAA1622, which we have renamed PP4R4."
- file:HORSE/PPP4R4/PPP4R4-bioinformatics/RESULTS.md: "share 95.0% identity among 865 paired residues. Paired coverage is 99.1% of human and 100.0% of horse."
COR — Correct novel prediction Review score: 2/2
Prediction method: ProtNLM2 · Version: UniProt API snapshot 2026-09-08
Review rationale: Human PP4R4 is an experimentally isolated stable cytosolic partner of PP4c and changes the activity of the complex. The selected horse protein is 95.0% identical across nearly the entire human sequence with no large domain deletion, supporting conserved complex membership and regulatory function. These claims are new relative to the frozen horse GOA; human evidence is not claimed to be absent from model training.
Supporting Evidence:
- PMID:18715871: "we identify a novel, stable cytosolic PP4c interacting partner, KIAA1622, which we have renamed PP4R4."
- PMID:18715871: "PP4c.PP4R4 complexes exhibit phosphatase activity toward a fluorogenic substrate and gammaH2AX, but this activity is lower than that associated with the PP4c.PP4R2.PP4R3 complex, which itself is less active than the free PP4c catalytic subunit."
- file:HORSE/PPP4R4/PPP4R4-bioinformatics/RESULTS.md: "share 95.0% identity among 865 paired residues. Paired coverage is 99.1% of human and 100.0% of horse."
COR — Correct novel prediction Review score: 2/2
Prediction method: ProtNLM2 · Version: UniProt API snapshot 2026-09-08
Review rationale: Human PP4R4 is an experimentally isolated stable cytosolic partner of PP4c and changes the activity of the complex. The selected horse protein is 95.0% identical across nearly the entire human sequence with no large domain deletion, supporting conserved complex membership and regulatory function. These claims are new relative to the frozen horse GOA; human evidence is not claimed to be absent from model training.
Supporting Evidence:
- PMID:18715871: "we identify a novel, stable cytosolic PP4c interacting partner, KIAA1622, which we have renamed PP4R4."
- PMID:18715871: "PP4c.PP4R4 complexes exhibit phosphatase activity toward a fluorogenic substrate and gammaH2AX, but this activity is lower than that associated with the PP4c.PP4R2.PP4R3 complex, which itself is less active than the free PP4c catalytic subunit."
- file:HORSE/PPP4R4/PPP4R4-bioinformatics/RESULTS.md: "share 95.0% identity among 865 paired residues. Paired coverage is 99.1% of human and 100.0% of horse."