id: P52037
gene_symbol: ygfF
locus_tag: b2898
taxon:
  id: NCBITaxon:83333
  label: Escherichia coli K-12
status: COMPLETE
description: >-
  YgfF DeepECTF prediction review. The DeepECTF prediction of glucose 1-dehydrogenase
  (EC 1.1.1.47) is a successful prediction, validated by SDR nomenclature classification
  (SDR63C subgroup) and consistent with published biochemical data.
references:
  - id: PMID:37963869
    title: Functional annotation of enzyme-encoding genes using deep learning with transformer layers.
  - id: PMID:40703034
    title: Limitations of current machine learning models in predicting enzymatic functions for uncharacterized
      proteins.
predictions:
  - source_method: DeepECTF
    source_version: "2023"
    source_reference_id: PMID:37963869
    predicted_term:
      id: EC:1.1.1.47
      label: glucose 1-dehydrogenase
    predicted_term_type: EC
    review:
      assessment: COR
      confidence_score: 2
      summary: >-
        Correct prediction. YgfF belongs to the SDR63C/Glucose 1-dehydrogenase subgroup
        of the SDR superfamily (IPR002347), as classified by the Oppermann/Persson HMM-based
        nomenclature system. The DeepECTF prediction matches this classification and was
        validated by in vitro assay. However, the actual in vivo substrate is NAD+ not NADP+,
        and the physiological substrate may be D-gluconate rather than glucose.
      supported_by:
        - reference_id: PMID:40703034
          supporting_text: "YgfF is a member of the large short-chain dehydrogenase/reductase (SDR) superfamily (IPR002347)...This resource predicts YgfF is part of the SDR63C/Glucose 1-dehydrogenase subgroup, the activity predicted and validated in the Kim et al. (2023) study. This prediction demonstrates the accurate propagation of functional annotation and is a successful prediction."