id: Q88KX9
gene_symbol: queF
taxon:
  id: NCBITaxon:160488
  label: Pseudomonas putida KT2440
status: COMPLETE
locus_tag: PP_2160
description: >-
  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.
references:
- id: PMID:33270901
  title: 'RefSeq: expanding the Prokaryotic Genome Annotation Pipeline reach with protein family model curation.'
- id: PMID:15767583
  title: 'From cyclohydrolase to oxidoreductase: discovery of nitrile reductase activity in a common fold.'
- id: file:PSEPK/queF/queF-uniprot.txt
  title: UniProtKB entry for queF (Q88KX9)
- id: file:PSEPK/queF/queF-pgap-prediction-evidence/WP_010953147.1.gp
  title: RefSeq GenPept record WP_010953147.1
- id: file:PSEPK/queF/queF-pgap-prediction-evidence/pgap_models.yaml
  title: PGAP naming model and matched NCBI HMMs for queF
source_documents:
- genes/PSEPK/queF/queF-pgap-prediction-evidence/WP_010953147.1.gp
- genes/PSEPK/queF/queF-pgap-prediction-evidence/pgap_models.yaml
predictions:
- source_method: NCBI PGAP
  source_version: GCF_000007565.2-RS_2026_02_04 (live); GO from WP_ record
  source_reference_id: PMID:33270901
  predicted_term:
    id: GO:0033739
    label: preQ1 synthase activity
  predicted_term_type: GO_MF
  review:
    assessment: CNN
    confidence_score: 2
    summary: >-
      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.
    supported_by:
    - reference_id: file:PSEPK/queF/queF-uniprot.txt
      supporting_text: "FUNCTION: Catalyzes the NADPH-dependent reduction of 7-cyano-7-"
    - reference_id: PMID:15767583
      supporting_text: "the NADPH-dependent reduction of 7-cyano-7-deazaguanineto7-aminomethyl-7-deazaguanine, a late step in the biosynthesis of queuosine"
- source_method: NCBI PGAP
  source_version: GCF_000007565.2-RS_2026_02_04 (live); GO from WP_ record
  source_reference_id: PMID:33270901
  predicted_term:
    id: GO:0043867
    label: 7-cyano-7-deazaguanine tRNA-ribosyltransferase activity
  predicted_term_type: GO_MF
  review:
    assessment: NPI
    confidence_score: 0
    error_type: CURATION_MISTAKE
    summary: >-
      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.
    supported_by:
    - reference_id: file:PSEPK/queF/queF-uniprot.txt
      supporting_text: "deazaguanine (preQ0) to 7-aminomethyl-7-deazaguanine (preQ1)."
    - reference_id: PMID:15767583
      supporting_text: "Contrary to the predictions based on sequence analysis, we discovered that the enzymes, in fact, catalyze a mechanistically unrelated reaction"
- source_method: NCBI PGAP
  source_version: GCF_000007565.2-RS_2026_02_04 (live); GO from WP_ record
  source_reference_id: PMID:33270901
  predicted_term:
    id: GO:0008616
    label: tRNA queuosine(34) biosynthetic process
  predicted_term_type: GO_BP
  review:
    assessment: CNN
    confidence_score: 2
    summary: >-
      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.
    supported_by:
    - reference_id: file:PSEPK/queF/queF-uniprot.txt
      supporting_text: "PATHWAY: tRNA modification; tRNA-queuosine biosynthesis."
- source_method: NCBI PGAP
  source_version: GCF_000007565.2-RS_2026_02_04 (live); GO from WP_ record
  source_reference_id: PMID:33270901
  predicted_term:
    id: EC:1.7.1.13
    label: EC 1.7.1.13
  predicted_term_type: EC
  review:
    assessment: CNN
    confidence_score: 2
    summary: >-
      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.
    supported_by:
    - reference_id: file:PSEPK/queF/queF-uniprot.txt
      supporting_text: "carbaguanine + 2 NADPH + 3 H(+); Xref=Rhea:RHEA:13409,"