These computational predictions are reviewed separately from the GOA annotation set used for this review. The assessments below are from this project and do not constitute official GO annotations or endorsement by GO/UniProt. They are not included in the existing annotation review above.
ProtNLM2 External predictions
View prediction review YAML · DUOX1-protnlm-predictions-review.yaml · Review status: COMPLETE
ProtNLM2 emitted four GO terms for A0A9L0SQG9, an alternative horse DUOX1 splice product (PTHR11972:SF75) that lacks human residues 775-873, removing EF-hand 1 and most of EF-hand 2 while keeping the peroxidase-homology domain, all transmembrane helices and every heme, FAD and NADPH contact residue. Calcium ion binding is correct and not novel, since the canonical horse DUOX1 product F6YEX2 carries it, and it has exact-sequence support from the conserved putative calcium site in the peroxidase-homology domain. Thyroid hormone generation is true of the gene but uncertain for this product. DUOX1 joins the process through H2O2 production, the product keeps the whole catalytic core but lacks the calcium-sensing EF-hands that activate it, and calcium-free DUOX1 still shows low basal activity, so the deletion's effect on H2O2 output is untested. Hydrogen peroxide catabolic process is refuted, because DUOX1 generates H2O2 and its peroxidase-homology domain has no peroxidase activity. Hormone biosynthetic process is refuted by GO semantics, because the only hormone pathway DUOX1 supports, thyroid hormone generation, is explicitly excluded from biosynthetic processes.
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/DUOX1.json
Review score: 2 = concordant with evidence; 1 = uncertain; 0 = discordant with evidence. This is an assessment score, not a model probability.
Prediction method: ProtNLM2 · Version: UniProt API snapshot 2026-09-08
Review rationale: DUOX1's only established hormone-related role is supplying the H2O2 that thyroid peroxidase uses to iodinate thyroglobulin, which GO captures as thyroid hormone generation (GO:0006590), a term the canonical horse DUOX1 product F6YEX2 already carries. GO deliberately places thyroid hormone generation outside the biosynthetic-process branch; OLS4 shows GO:0006590 is not a descendant of GO:0042446, and its definition comment states that the term does not fall under the general GO definition for biosynthetic processes because thyroid hormones are formed by proteolysis of a larger molecule. No evidence links DUOX1 to the biosynthesis of any other hormone. The prediction therefore places a real thyroid contribution under a GO branch that excludes it, and the term is discordant with GO's definition of the process DUOX1 supports.
Supporting Evidence: - PMID:15062544: "A crucial step in thyroid hormone synthesis is the oxidative coupling of iodide to thyroglobulin that is catalyzed by thyroperoxidase. The limiting factor of this reaction is the supply of hydrogen peroxide."
- PMID:33420071: "Dual oxidases (DUOXs) produce hydrogen peroxide by transferring electrons from intracellular NADPH to extracellular oxygen."
Prediction method: ProtNLM2 · Version: UniProt API snapshot 2026-09-08
PSEUDOENZYME OVERANNOTATION
Review rationale: The mammalian DUOX1 catalytic system generates H2O2; the isolated human peroxidase-like domain binds no heme and has no intrinsic peroxidase activity. Producing the substrate for a separate peroxidase is not evidence that DUOX1 carries out H2O2 catabolism. The selected horse protein retains the homologous peroxidase-like region within the same DUOX1 subfamily as human DUOX1, and no independent catabolic mechanism is supported. The gene review removes the electronic peroxidase activity and cellular oxidant detoxification rows on these grounds. This prediction confuses an oxidant-generating enzyme with peroxide-consuming chemistry.
Supporting Evidence: - PMID:19460756: "the isolated hDUOX1(1-593) does not bind heme and has no intrinsic peroxidase activity."
- PMID:33420071: "Dual oxidases (DUOXs) produce hydrogen peroxide by transferring electrons from intracellular NADPH to extracellular oxygen."
- file:HORSE/DUOX1/DUOX1-bioinformatics/RESULTS.md: "share 91.4% identity among 1452 paired residues. Paired coverage is 93.6% of human and 100.0% of horse."
Prediction method: ProtNLM2 · Version: UniProt API snapshot 2026-09-08
Review rationale: Thyroid hormone generation is a correct term for the DUOX1 gene, and the canonical horse product F6YEX2 already carries it. DUOX1 takes part in the process by generating the H2O2 that thyroid peroxidase uses. A0A9L0SQG9 lacks the segment corresponding to human residues 775-873, which removes EF-hand 1 and most of EF-hand 2; of the 15 human calcium-ligand positions it keeps 6, and 5 of those form the extracellular peroxidase-homology site, not the EF-hands. The catalytic machinery is intact, with all heme, FAD and NADPH contact residues retained. The EF-hand module is a calcium-gated activator, not the catalytic step itself; point mutations of its calcium-binding residues abolish activity of mouse DUOX1-DUOXA1, but human DUOX1-DUOXA1 in low calcium retains low basal H2O2 production, and no study has tested a DUOX1 lacking this segment. The participation mechanism is therefore not fully accounted for by the missing feature, and there is no positive refutation; the product could retain basal or calcium-independent oxidase output, or could be inactive or fail to mature with DUOXA1. Whether this exact sequence contributes to thyroid hormone generation is unresolved.
Supporting Evidence: - PMID:32929281: "DUOX1 contains cytoplasmic EF-hand motifs, and mutations of calcium-binding residues abolish enzymatic activities of DUOX1–DUOXA1 complexes"
- PMID:33420071: "In the presence of calcium ions, intracellular EF-hand modules might enhance the catalytic activity of DUOX by stabilizing the dehydrogenase domain in a conformation that allows electron transfer."
- PMID:10806195: "Two cDNAs encoding NADPH oxidases and constituting the thyroid H(2)O(2) generating system have been cloned."
- file:HORSE/DUOX1/DUOX1-bioinformatics/RESULTS-rereview.md: "| A0A9L0SQG9 | 1452 | PTHR11972:SF75;PTHR11972 | ENSECAT00000123284 | False | 91.4% | 1-1551 | 775-873 | Ca(2+) 6/15; heme 13/13; FAD 8/8; NADPH 11/11 |"
- PMID:33420071: "In the low-calcium condition, DUOX1–DUOXA1 complex showed low basal activity"
Prediction method: ProtNLM2 · Version: UniProt API snapshot 2026-09-08
Review rationale: Calcium binding is directly observed in human DUOX1, whose EF-hand calcium occupancy switches the oxidase on, and horse DUOX1 already carries calcium ion binding on its canonical product F6YEX2, so the term is not novel for the gene. This splice product lacks EF-hand 1 and most of EF-hand 2, retaining 6 of the 15 human calcium-ligand positions. The retained ligands include the complete putative calcium site in the extracellular peroxidase-homology domain (human positions 109, 170, 172, 174 and 176), which the mouse DUOX1 structure places at the position of the lactoperoxidase calcium site, and the peroxidase-like region is fully present. Calcium ion binding is therefore supported for this exact sequence as well, by orthology within PTHR11972:SF75; what the deletion probably removes is calcium-regulated activation, not all calcium binding.
Supporting Evidence: - PMID:33420071: "In the presence of calcium ions, intracellular EF-hand modules might enhance the catalytic activity of DUOX by stabilizing the dehydrogenase domain in a conformation that allows electron transfer."
- PMID:32929281: "The structure also revealed two putative cation binding sites in the PHD of DUOX1. One likely accommodates a calcium ion, since it is located in the same position where the calcium-binding site of LPO is"
- file:HORSE/DUOX1/DUOX1-bioinformatics/RESULTS-rereview.md: "| A0A9L0SQG9 | 1452 | PTHR11972:SF75;PTHR11972 | ENSECAT00000123284 | False | 91.4% | 1-1551 | 775-873 | Ca(2+) 6/15; heme 13/13; FAD 8/8; NADPH 11/11 |"
- file:HORSE/DUOX1/DUOX1-bioinformatics/RESULTS-rereview.md: "| Peroxidase-like (26-593) | 1.00 | 1.00 | 0.94 | 1.00 |"