id: Q9L243
gene_symbol: SCO2678
taxon:
  id: NCBITaxon:100226
  label: Streptomyces coelicolor
status: COMPLETE
description: >-
  The HAD_SAK_2 domain assignment supports a phosphatase-family hypothesis, but nucleotide substrate specificity
  and deoxyribonucleotide catabolism are unresolved.
source_documents:
  - genes/STRCO/Q9L243/Q9L243-uniprot.txt
  - genes/STRCO/Q9L243/Q9L243-goa.tsv
  - genes/STRCO/Q9L243/Q9L243-hypotheses/prediction-deoxyribonucleotide-catabolism/openscientist.md
predictions:
  - source_method: ProtNLM2
    source_version: UniProt 2024_06 pilot
    predicted_term:
      id: GO:0008253
      label: 5'-nucleotidase activity
    predicted_term_type: GO_MF
    review:
      assessment: UNC
      confidence_score: 1
      summary: >-
        The 171-residue target has a Pfam HAD_SAK_2 assignment and intact HAD-family phosphohydrolase
        motifs, but the focused report found no specific nucleotidase signature or characterized dNMP-acting
        subfamily relationship. The fold supports a low-specificity phosphatase hypothesis; it does not
        establish that the substrate is a nucleotide or that phosphate is removed at its 5-prime position.
        The inspected sources contain no target substrate assay or well-resolved experimentally characterized
        ortholog establishing that specificity. The predicted activity is absent from the cached annotations
        and remains uncertain.
      supported_by:
        - reference_id: file:STRCO/Q9L243/Q9L243-uniprot.txt
          supporting_text: >-
            ID   Q9L243_STRCO            Unreviewed;       171 AA. ... DR   Pfam; PF18143; HAD_SAK_2;
            1.
        - reference_id: file:STRCO/Q9L243/Q9L243-hypotheses/prediction-deoxyribonucleotide-catabolism/openscientist.md
          supporting_text: >-
            GO:0008253 (5′-nucleotidase activity, MF): treat as unproven / too specific.
  - source_method: ProtNLM2
    source_version: UniProt 2024_06 pilot
    predicted_term:
      id: GO:0009264
      label: deoxyribonucleotide catabolic process
    predicted_term_type: GO_BP
    review:
      assessment: NPI
      error_type: FREQUENCY_BIAS
      confidence_score: 0
      summary: >-
        A HAD-family domain can motivate a phosphatase hypothesis but does not identify deoxyribonucleotides
        as physiological substrates. The focused report found that SCO2678 belongs to the PF18143 RNA-repair-associated
        HAD family rather than characterized dNMP-acting nucleotidase subfamilies, has no nucleotide-catabolism
        genomic context, and lacks target biochemical or pathway evidence. ProtNLM2 overextended a generic
        HAD phosphatase signal to a 5-prime-nucleotidase label and then to a pathway-level deoxyribonucleotide
        catabolic-process term. The predicted process is absent from the cached annotations and is too specific
        for the inspected evidence.
      supported_by:
        - reference_id: file:STRCO/Q9L243/Q9L243-uniprot.txt
          supporting_text: >-
            ID   Q9L243_STRCO            Unreviewed;       171 AA. ... DR   Pfam; PF18143; HAD_SAK_2;
            1.
        - reference_id: file:STRCO/Q9L243/Q9L243-hypotheses/prediction-deoxyribonucleotide-catabolism/openscientist.md
          supporting_text: >-
            GO:0009264 (deoxyribonucleotide catabolic process, BP): do not assign / remove as core.
references:
  - id: file:STRCO/Q9L243/Q9L243-uniprot.txt
    title: Q9L243-uniprot.txt
  - id: file:STRCO/Q9L243/Q9L243-hypotheses/prediction-deoxyribonucleotide-catabolism/openscientist.md
    title: openscientist.md