id: Q7CR11
gene_symbol: ybbO
locus_tag: STM0505
taxon:
  id: NCBITaxon:99287
  label: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
status: COMPLETE
description: >-
  The KBase gene-annotate dashboard predicted "Short-chain
  dehydrogenase/reductase (SDR) family oxidoreductase, substrate undetermined"
  with one GO term, GO:0016491 oxidoreductase activity, for Salmonella enterica
  gene AYCY01000026.1_161 (serovar not stated). The query is scored on Q7CR11,
  and the taxon above is that accession's. The two sequences are 99.6%
  identical over all 256 residues, differing only at I244L, a conservative
  change away from the catalytic residues. The query is a catalytically intact
  classical SDR: TGxxxGxG cofactor motif at residue 8, NNAG at 80, and YxxxK
  with Tyr146/Lys150. Its E. coli orthologue YbbO (P0AFP4) is 91.0% identical
  over the query length by global alignment (233/256). The 90.6% in the
  companion review is the same comparison for Q7CR11, which matches P0AFP4 at
  one fewer position. E. coli YbbO is an NADP(+)-dependent aldehyde reductase
  with kinetics on C6-C18 aldehydes (PMID:27134112), and it was among five new
  aldehyde reductases found in a 44-candidate screen (PMID:25108218). The
  prediction is correct but not novel, because GO:0016491 is already in GOA as
  an IBA. It is also less informative than the orthologue evidence allows: the
  companion review refines that row to GO:0008106 alcohol dehydrogenase (NADP+)
  activity.
source_documents:
- genes/SALTY/ybbO/ybbO-dashboard-prediction-evidence/prediction.json
- genes/SALTY/ybbO/ybbO-dashboard-prediction-evidence/identity_results.json
references:
- id: file:SALTY/ybbO/ybbO-dashboard-prediction-evidence/prediction.json
  title: gene-annotate dashboard prediction for AYCY01000026.1_161
  findings:
  - statement: The prediction is a family-level SDR oxidoreductase with no substrate.
    supporting_text: Short-chain dehydrogenase/reductase (SDR) family oxidoreductase, substrate undetermined.
- id: file:SALTY/ybbO/ybbO-dashboard-prediction-evidence/identity_results.json
  title: Identity and SDR motif analysis of AYCY01000026.1_161 (BERIL run 20261031T002028Z-ybbo-dashboard-identity)
  findings:
  - statement: The query differs from Q7CR11 at a single position.
    supporting_text: '"label": "S. Typhimurium LT2 STM0505" ... "I244L"'
  - statement: The query is 91.0% identical to E. coli YbbO over its full length by global alignment.
    supporting_text: '"label": "E. coli K-12 YbbO" ... "percent_identity_over_query_length": 91.0'
- id: PMID:27134112
  title: Identification of long chain specific aldehyde reductase and its use in enhanced fatty alcohol production in E. coli.
  findings:
  - statement: E. coli YbbO is an NADP(+)-dependent aldehyde reductase with broad aldehyde chain-length specificity.
    supporting_text: Enzyme kinetic study revealed that YbbO has wide substrate specificity ranging from C6 to C18 aldehyde, with maximum affinity and efficiency for C18 and C16 chain length aldehyde, respectively.
- id: PMID:25108218
  title: Toward aldehyde and alkane production by removing aldehyde reductase activity in Escherichia coli.
  findings:
  - statement: YbbO was identified as an E. coli aldehyde reductase in a screen of 44 candidate oxidoreductases.
    supporting_text: From the pool of 44 candidates, we found five new ALRs using this screening method (YahK, DkgA, GldA, YbbO, and YghA).
predictions:
- source_method: gene-annotate dashboard LLM annotation (Dark Protein Atlas)
  source_version: '2026-10-30 snapshot'
  predicted_term:
    id: GO:0016491
    label: oxidoreductase activity
  predicted_term_type: GO_MF
  review:
    assessment: CNN
    confidence_score: 2
    summary: >-
      The prediction is biologically correct. The query is a catalytically intact
      classical SDR (TGxxxGxG at residue 8, NNAG at 80, Tyr146/Lys150 in the YxxxK
      motif; identity_results.json). Its 91.0%-identical E. coli orthologue YbbO
      is an experimentally characterized NADP(+)-dependent aldehyde reductase
      (PMID:27134112, PMID:25108218). GO:0016491 is already in GOA for Q7CR11 as
      an IBA, so it is not novel. LSP is not used because GOA holds no more
      specific curated term. The companion review refines the IBA row to
      GO:0008106 alcohol dehydrogenase (NADP+) activity by orthology, which this
      prediction does not capture.
    supported_by:
    - reference_id: PMID:27134112
      supporting_text: Enzyme kinetic study revealed that YbbO has wide substrate specificity ranging from C6 to C18 aldehyde, with maximum affinity and efficiency for C18 and C16 chain length aldehyde, respectively.
    - reference_id: file:SALTY/ybbO/ybbO-dashboard-prediction-evidence/identity_results.json
      supporting_text: '"label": "E. coli K-12 YbbO" ... "percent_identity_over_query_length": 91.0'