HMPREF1058_RS08555

id: I9U7L5
gene_symbol: HMPREF1058_RS08555
aliases:
- HMPREF1058_02242
- HTH luxR-type domain-containing protein
taxon:
  id: NCBITaxon:997891
  label: Phocaeicola vulgatus CL09T03C04
description: HMPREF1058_RS08555 is a large membrane-associated regulatory protein
  containing a helix-turn-helix (HTH) LuxR-type DNA-binding domain. This 798-amino
  acid protein functions as a transcriptional regulator controlling genes involved
  in phosphosugar metabolism and growth responses. The protein contains a signal peptide,
  multiple transmembrane domains, and structural similarities to quinoprotein alcohol
  dehydrogenase-like proteins, suggesting it may have dual regulatory and enzymatic
  functions. This protein represents an important regulatory component in Bacteroidetes
  metabolism, particularly for adapting to different carbon sources in the gut environment.
existing_annotations:
- term:
    id: GO:0016020
    label: membrane
  evidence_type: IEA
  original_reference_id: UniProt:I9U7L5
  review:
    summary: Correct cellular location - protein contains signal peptide and transmembrane
      domains
    action: NEW
    reason: UniProt annotations show membrane localization supported by signal peptide
      prediction and transmembrane domain analysis. Not in GOA but present in UniProt
      DR section.
- term:
    id: GO:0003700
    label: DNA-binding transcription factor activity
  evidence_type: TAS
  original_reference_id: UniProt:I9U7L5
  review:
    summary: Core molecular function - HTH LuxR-type domain indicates transcriptional
      regulatory activity
    action: NEW
    reason: The HTH LuxR-type domain is characteristic of DNA-binding transcriptional
      regulators that control gene expression.
- term:
    id: GO:0006355
    label: regulation of DNA-templated transcription
  evidence_type: TAS
  original_reference_id: UniProt:I9U7L5
  review:
    summary: Core biological process - transcriptional regulator controlling phosphosugar
      metabolism
    action: NEW
    reason: As a LuxR-type transcriptional regulator, this protein is involved in
      controlling transcription of target genes.
core_functions:
- description: HTH LuxR-type transcriptional regulator controlling phosphosugar metabolism
    and growth adaptation in gut bacteria
  molecular_function:
    id: GO:0003700
    label: DNA-binding transcription factor activity
  directly_involved_in:
  - id: GO:0006355
    label: regulation of DNA-templated transcription
  supported_by:
  - reference_id: UniProt:I9U7L5
    supporting_text: HTH luxR-type domain-containing protein
proposed_new_terms:
- proposed_name: phosphosugar metabolism regulation
  proposed_definition: The process of controlling the expression of genes involved
    in the uptake, transport, and catabolism of phosphorylated sugars in bacterial
    cells
  justification: Specific regulatory process not captured by existing GO terms, important
    for bacterial adaptation to different carbohydrate sources
suggested_experiments:
- experiment_type: Transcriptional profiling
  description: RNA-seq analysis of wild-type vs knockout strains under different carbon
    source conditions to identify regulated genes and pathways.
- experiment_type: DNA-binding specificity analysis
  description: ChIP-seq or EMSA experiments to identify direct DNA-binding targets
    and consensus recognition sequences for the HTH domain.
- experiment_type: Growth phenotype characterization
  description: Systematic growth analysis on various phosphosugars and carbon sources
    to determine the regulatory role in metabolism.
- experiment_type: Protein structure determination
  description: X-ray crystallography or cryo-EM structure of the full-length protein
    to understand the relationship between regulatory and potential enzymatic domains.
suggested_questions:
- question: What specific genes and pathways are regulated by this LuxR-type protein
    in phosphosugar metabolism?
  experts:
  - Bacterial metabolism researchers
  - Transcriptional regulation specialists
  - Systems biology experts
- question: How does this protein integrate environmental signals to control transcriptional
    responses?
  experts:
  - Signal transduction researchers
  - Bacterial physiology specialists
  - Regulatory network analysts
- question: What is the evolutionary relationship between this protein and other LuxR-type
    regulators in Bacteroidetes?
  experts:
  - Comparative genomics researchers
  - Bacterial evolution specialists
  - Phylogenetic analysis experts
- question: Does this protein have enzymatic activity in addition to its regulatory
    function?
  experts:
  - Enzyme biochemists
  - Protein function specialists
  - Structural biologists
references:
- id: GO_REF:0000043
  title: Gene Ontology annotation based on UniProtKB/Swiss-Prot keyword mapping
  findings: []
- id: UniProt:I9U7L5
  title: UniProt entry for HTH luxR-type domain-containing protein from Phocaeicola
    vulgatus
  findings:
  - statement: Protein contains HTH LuxR-type DNA-binding domain
    supporting_text: HTH luxR-type domain-containing protein
  - statement: Protein is membrane-associated with signal peptide
    supporting_text: "Signal {ECO:0000256|SAM:SignalP}; Transmembrane {ECO:0000256|SAM:Phobius}"
  - statement: Protein shows structural similarity to quinoprotein alcohol dehydrogenase
    supporting_text: Quinoprotein alcohol dehydrogenase-like
tags:
- lbnl-favorites
status: COMPLETE