id: P0AFJ1
gene_symbol: yjdM
locus_tag: b4108
taxon:
  id: NCBITaxon:83333
  label: Escherichia coli K-12
status: COMPLETE
description: >-
  YjdM DeepECTF prediction review. The DeepECTF prediction of phosphonoacetate hydrolase
  (EC 3.11.1.2) was validated in vitro but is uncertain for in vivo function. The in vitro
  PhnA activity may not represent the biological function - genome neighborhood analysis
  shows yjdM genes are generally not near phosphonate catabolism genes except in E. coli,
  and the experimentally validated PhnA belongs to a nonhomologous family.
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:3.11.1.2
      label: phosphonoacetate hydrolase
    predicted_term_type: EC
    review:
      assessment: UNC
      confidence_score: 1
      error_type: IN_VITRO_NOT_IN_VIVO
      summary: >-
        Uncertain. YjdM was shown to catalyze phosphonoacetate hydrolase activity in vitro,
        but multiple lines of evidence suggest this is not its biological function:
        (1) The initial report linking YjdM to phosphonate catabolism was refuted by
        additional genetic analyses (Metcalf and Wanner 1993).
        (2) The experimentally validated PhnA belongs to a nonhomologous family, and
        expression of that family in E. coli showed PhnA activity was absent.
        (3) Genome neighborhood analysis shows yjdM genes are generally NOT near
        phosphonate catabolism or transport genes except in E. coli, where it happens
        to be upstream of the phn operon.
        (4) True phnA genes cluster with phosphonoacetate transporters and regulators.
        The in vitro activity may represent promiscuous hydrolytic activity rather than
        the evolved biological function.
      supported_by:
        - reference_id: PMID:40703034
          supporting_text: "except for E. coli, yjdM genes are generally not close to phosphonate catabolism or transport genes"
        - reference_id: PMID:40703034
          supporting_text: "the PhnA activity observed in vitro is not supported, and additional in vivo experiments are required to confirm the biological role of this enzyme. This prediction was given a CS of 1"