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.
NCBI PGAP External predictions
View prediction review YAML · queF-pgap-predictions-review.yaml · Review status: COMPLETE
NCBI PGAP names WP_010953147.1 "NADPH-dependent 7-cyano-7-deazaguanine reductase QueF" from the TIGR03138 equivalog HMM and passes on that model's EC 1.7.1.13 and three GO terms. The name, the EC number, preQ1 synthase activity and tRNA queuosine biosynthesis all agree with the reviewed UniProt entry and the main review. The third GO term, 7-cyano-7-deazaguanine tRNA-ribosyltransferase activity (GO:0043867), is wrong: it is the archaeal TgtA reaction that inserts preQ0 into tRNA, a different enzyme acting on the same small molecule. QueF reduces free preQ0 to preQ1 and does not touch tRNA. The error lies in the GO mapping of the TIGR03138 model itself, so every QueF named by that model receives it; the PfamEq model NF025842 for the same protein carries only the two correct terms.
Source documents: genes/PSEPK/queF/queF-pgap-prediction-evidence/WP_010953147.1.gp · genes/PSEPK/queF/queF-pgap-prediction-evidence/pgap_models.yaml
Review score: 2 = concordant with evidence; 1 = uncertain; 0 = discordant with evidence. This is an assessment score, not a model probability.
Prediction method: NCBI PGAP · Version: GCF_000007565.2-RS_2026_02_04 (live); GO from WP_ record ·
PMID:33270901 Review rationale: Correct and already in GOA (UniRule IEA), where the main review accepts it as QueF's core activity. Q88KX9 is a reviewed type 2 QueF, and the characterized B. subtilis and E. coli enzymes catalyse exactly this NADPH-dependent nitrile reduction.
Supporting Evidence: - file:PSEPK/queF/queF-uniprot.txt: "FUNCTION: Catalyzes the NADPH-dependent reduction of 7-cyano-7-"
- PMID:15767583: "the NADPH-dependent reduction of 7-cyano-7-deazaguanineto7-aminomethyl-7-deazaguanine, a late step in the biosynthesis of queuosine"
Prediction method: NCBI PGAP · Version: GCF_000007565.2-RS_2026_02_04 (live); GO from WP_ record ·
PMID:33270901 CURATION MISTAKE
Review rationale: Wrong. GO:0043867 is defined as tRNA guanine + 7-cyano-7-deazaguanine = tRNA 7-cyano-7-deazaguanine + guanine, the base-exchange reaction of the archaeal tRNA-guanine transglycosylase TgtA (synonyms TgtA, archaeal tRNA-guanine transglycosylase activity). That activity belongs to a different enzyme in a different lineage. QueF instead reduces free preQ0 to preQ1, which the bacterial Tgt then inserts into tRNA; QueF has no tRNA-ribosyltransferase activity. The shared substrate name (7-cyano-7-deazaguanine) is the likely source of the confusion. The wrong term sits on the TIGR03138 model's GO list next to the correct preQ1 synthase term, so the error is on the HMM and reaches every genome; the PfamEq model NF025842 lists only GO:0008616 and GO:0033739.
Supporting Evidence: - file:PSEPK/queF/queF-uniprot.txt: "deazaguanine (preQ0) to 7-aminomethyl-7-deazaguanine (preQ1)."
- PMID:15767583: "Contrary to the predictions based on sequence analysis, we discovered that the enzymes, in fact, catalyze a mechanistically unrelated reaction"
Prediction method: NCBI PGAP · Version: GCF_000007565.2-RS_2026_02_04 (live); GO from WP_ record ·
PMID:33270901 Review rationale: Correct and already in GOA, where the main review accepts it (and proposes it as the replacement for the broader tRNA modification term). QueF makes preQ1, the base that Tgt inserts at tRNA position 34. The GenPept record shows the older label "queuosine biosynthetic process" for the same id.
Prediction method: NCBI PGAP · Version: GCF_000007565.2-RS_2026_02_04 (live); GO from WP_ record ·
PMID:33270901 Review rationale: Correct and not novel: EC 1.7.1.13 (preQ1 synthase) is the EC number on the reviewed UniProt entry (HAMAP MF_00817) and matches the accepted GO:0033739.