ProtNLM2 External predictions
View prediction review YAML · GEMIN5-protnlm-predictions-review.yaml · Review status: COMPLETE
A0A9L0R5P7 is an alternative-transcript product of horse GEMIN5 that keeps the complete tandem WD40 snRNA/cap-recognition module and the C-terminal RNA-binding regions, and lacks only a disordered linker equivalent to human 723-798, which contains the protein's lysine-rich basic cluster (horse F6WDM0 748-757). Three ProtNLM2 predictions (spliceosomal snRNP assembly, RNA 7-methylguanosine cap binding, regulation of translation) depend on regions this product retains, are supported by human ortholog experiments within the same PANTHER subfamily, and are already carried by this gene in GOA (CNN). Nucleus and mRNA 3'-UTR binding are true of the gene but depend on determinants that have not been mapped, so whether the deleted basic linker is needed for them on this product is unresolved (UNC). Protein ubiquitination has no supporting evidence for GEMIN5 or its relatives (UNC).
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/GEMIN5.json · genes/HORSE/GEMIN5/GEMIN5-ai-review.yaml · genes/HORSE/GEMIN5__F6WDM0/GEMIN5__F6WDM0-ai-review.yaml
Review score: 2 = concordant with evidence; 1 = uncertain; 0 = discordant with evidence. This is an assessment score, not a model probability.
CNN — Correct but not novel Review score: 2/2
Prediction method: ProtNLM2 · Version: UniProt API snapshot 2026-09-08
Review rationale: Human GEMIN5 binds the Sm site of snRNAs through its tandem WD40 domain and is required for SMN-complex Sm-core assembly. A0A9L0R5P7 is in the same PANTHER subfamily (PTHR46362:SF1), shares 89% identity with human, and keeps the complete folded WD40 module (human 3-722) with all 12 mutationally validated RNA-contact residues; its missing block (human 723-798) is a disordered linker outside the fold. The transfer is therefore justified, as an inference from the human ortholog. The gene already carries this term in GOA on its full-length product F6WDM0 (IBA from PAINT and Ensembl Compara IEA), and the gene review lists it as a core process of this product, so the prediction is correct but not novel.
Supporting Evidence:
- PMID:16857593: "Reduction of Gemin5 results in"
- PMID:27881600: "the WD40 domain of Gemin5 is both necessary and sufficient for binding the Sm site of pre-snRNAs"
- PMID:27881601: "The 2.0 Å structure shows that the G5N region encompassing residues 3–722 is folded into two seven-bladed WD40 repeat domains."
- file:HORSE/GEMIN5/GEMIN5-uniprot.txt: "DR PANTHER; PTHR46362:SF1; GEM-ASSOCIATED PROTEIN 5; 1."
- file:HORSE/GEMIN5/GEMIN5-bioinformatics/rereview/RESULTS-rereview.md: "It therefore sits C-terminal to the structured RNA-recognition module, not inside it."
- file:HORSE/GEMIN5/GEMIN5-bioinformatics/rereview/RESULTS-rereview.md: "All 12 human residues mutated in PMID:27881601 (N13, W14, Y15, R33, R335, M357, R359, F381, Y383, M403, W422, Y474) are identical at the aligned positions in both A0A9L0R5P7 and F6WDM0."
UNC — Uncertain Review score: 1/2
Prediction method: ProtNLM2 · Version: UniProt API snapshot 2026-09-08
Review rationale: The characterised activities of GEMIN5 are snRNA and cap recognition for snRNP assembly, SMN mRNA 3'-UTR binding and ribosome-associated translation control. Neither the human nor the horse gene review, the GOA files of either horse product, nor a PubMed search for GEMIN5 with ubiquitin, ubiquitination or E3 (three hits, none describing a GEMIN5 role in ubiquitination) supports participation in protein ubiquitination. GEMIN5 has no ubiquitin-ligase or ubiquitin-binding domain, but the absence of a catalytic domain would not by itself refute a noncatalytic role. No evidence supports or refutes the prediction.
Supporting Evidence:
- PMID:27881600: "the WD40 domain of Gemin5 is both necessary and sufficient for binding the Sm site of pre-snRNAs"
- PMID:25911097: "Gemin5 binding to the SMN 3′-UTR activates expression of SMN protein by increasing translation of the SMN mRNA."
- file:HORSE/GEMIN5/GEMIN5-uniprot.txt: "DR PANTHER; PTHR46362:SF1; GEM-ASSOCIATED PROTEIN 5; 1."
UNC — Uncertain Review score: 1/2
Prediction method: ProtNLM2 · Version: UniProt API snapshot 2026-09-08
Review rationale: Immunolocalization of human GEMIN5 shows a minor nuclear pool that colocalizes with SMN in gems, besides the predominant cytoplasmic pool, so nucleus is true of the gene (and less specific than the nucleoplasm and Gemini of Cajal bodies annotations the gene carries). For this product the call is unresolved. A0A9L0R5P7 lacks the block equivalent to human 723-798, which in the full-length horse product F6WDM0 includes the basic-residue cluster at 748-757 (PKPKKKKK), a lysine run of the kind that can act as a classical monopartite nuclear localization signal; the product keeps a shorter KKRK motif at its residue 765. No nuclear-import determinant of GEMIN5 has been mapped, and its nuclear pool could instead depend on co-import with the SMN complex, so it cannot be told whether this product keeps what nuclear localization requires.
Supporting Evidence:
- PMID:11714716: "Immunolocalization studies demonstrate that Gemin5 is found in the cytoplasm and in the nucleus, where it colocalizes with SMN in gems."
- file:HORSE/GEMIN5/GEMIN5-bioinformatics/rereview/RESULTS-rereview.md: "It lacks a 76-residue internal block that corresponds to human 723-798."
- file:HORSE/GEMIN5__F6WDM0/GEMIN5__F6WDM0-uniprot.txt: "FT COMPBIAS 748..757"
- file:HORSE/GEMIN5/GEMIN5-uniprot.txt: "DR PANTHER; PTHR46362:SF1; GEM-ASSOCIATED PROTEIN 5; 1."
CNN — Correct but not novel Review score: 2/2
Prediction method: ProtNLM2 · Version: UniProt API snapshot 2026-09-08
Review rationale: Human GEMIN5 binds the m7G cap directly in pull-down assays, and a soaked m7GTP structure places the cap in the central pore of the second WD40 propeller, stacked by Tyr474 and contacted by Leu580 and Asn582. A0A9L0R5P7 keeps the complete folded WD40 module; the deletion lies C-terminal to it. A direct ungapped comparison of the downloaded sequences in this assessment shows the cap-site residues W286, F338, Y474, L580 and N582 identical to human. The transfer from the same PANTHER subfamily is therefore justified. The gene already carries this term in GOA on its full-length product F6WDM0 (Ensembl Compara IEA, accepted by its review), so the prediction is correct but not novel.
Supporting Evidence:
- PMID:19750007: "Gemin5 binds directly to the m7G cap structure."
- PMID:27881600: "the WD40 domain of Gemin5 recognizes the Sm site and m7G cap of pre-snRNAs via two distinct binding sites"
- PMID:27881601: "In the present structure, Tyr474 stacks m7G from one side, but the other side is contacted by Leu580 and Asn582."
- file:HORSE/GEMIN5/GEMIN5-uniprot.txt: "DR PANTHER; PTHR46362:SF1; GEM-ASSOCIATED PROTEIN 5; 1."
- file:HORSE/GEMIN5/GEMIN5-bioinformatics/rereview/RESULTS-rereview.md: "It therefore sits C-terminal to the structured RNA-recognition module, not inside it."
UNC — Uncertain Review score: 1/2
Prediction method: ProtNLM2 · Version: UniProt API snapshot 2026-09-08
Review rationale: Human GEMIN5 binds the SMN mRNA 3'-UTR directly, and PAINT places this activity at node PTN005299808, so the term is true of the gene, which carries it in GOA on both horse products. For this product the call is unresolved. A0A9L0R5P7 keeps the WD40 module and the C-terminal TPR-like and RBS regions, but lacks the block equivalent to human 723-798, which includes the lysine-rich basic cluster (F6WDM0 748-757), a type of segment that commonly contributes to RNA contacts. The SMN 3'-UTR binding interface has not been mapped to any region, so it cannot be told whether this product keeps what the activity requires.
Supporting Evidence:
- PMID:25911097: "Gemin5 directly binds to the mature SMN 3′-UTR immediately upstream of the poly(A) tail."
- file:HORSE/GEMIN5/GEMIN5-bioinformatics/rereview/RESULTS-rereview.md: "It lacks a 76-residue internal block that corresponds to human 723-798."
- file:HORSE/GEMIN5__F6WDM0/GEMIN5__F6WDM0-uniprot.txt: "FT COMPBIAS 748..757"
- file:HORSE/GEMIN5/GEMIN5-bioinformatics/rereview/RESULTS-rereview.md: "The analysis says nothing about the SMN 3'-UTR binding interface, which has not been mapped to a domain."
- file:HORSE/GEMIN5/GEMIN5-uniprot.txt: "DR PANTHER; PTHR46362:SF1; GEM-ASSOCIATED PROTEIN 5; 1."
CNN — Correct but not novel Review score: 2/2
Prediction method: ProtNLM2 · Version: UniProt API snapshot 2026-09-08
Review rationale: In human cells GEMIN5 binding to the SMN 3'-UTR increases SMN translation, and GEMIN5 bound to ribosomes through its N-terminal domain dampens global protein synthesis, so it regulates translation in both directions. The horse product keeps the relevant RNA-binding regions and is in the same PANTHER subfamily, which justifies transfer as an inference. The full-length product F6WDM0 already carries regulation of translation in GOA (Ensembl Compara IEA), and the gene review of this product uses the same term in its core functions, so the prediction is correct but not novel.
Supporting Evidence:
- PMID:25911097: "Gemin5 binding to the SMN 3′-UTR activates expression of SMN protein by increasing translation of the SMN mRNA."
- PMID:27507887: "His-Gemin5 binds to ribosome particles via its N-terminal domain."
- PMID:27507887: "enhanced global protein synthesis"
- file:HORSE/GEMIN5/GEMIN5-uniprot.txt: "DR PANTHER; PTHR46362:SF1; GEM-ASSOCIATED PROTEIN 5; 1."