Difference between revisions of "Sandbox"

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−
* '''Description:''' L-arabinose permease <br/><br/>
+
* '''Description:''' transcription repressor of the treP-treA-treR operon <br/><br/>
  
 
{| align="right" border="1" cellpadding="2"  
 
{| align="right" border="1" cellpadding="2"  
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"|'''Gene name'''
 
|style="background:#ABCDEF;" align="center"|'''Gene name'''
−
|''araE''
+
|''treR''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yvbR ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yfxA ''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || L-arabinose permease
+
|style="background:#ABCDEF;" align="center"| '''Product''' || transcription repressor
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || uptake of arabinose, galactose and xylose
+
|style="background:#ABCDEF;" align="center"|'''Function''' || regulaation of trehalose utilization
 
|-
 
|-
 
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: <br/>[http://subtiwiki.uni-goettingen.de/pathways/carbohydrate_metabolic_pathways.html Sugar catabolism]'''
 
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: <br/>[http://subtiwiki.uni-goettingen.de/pathways/carbohydrate_metabolic_pathways.html Sugar catabolism]'''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 50 kDa, 9.259  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 27 kDa, 6.82  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1392 bp, 464 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 714 bp, 238 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[cggR]]'', ''[[araR]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[treA]]'', ''[[yfkO]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB15401&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
+
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB12611&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:araE_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:treR_context.gif]]
 
  <div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
 
  <div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
 
|-
 
|-
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=== Basic information ===
 
=== Basic information ===
  
−
* '''Locus tag:''' BSU33960
+
* '''Locus tag:''' BSU07820
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
Line 43: Line 43:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' no entry
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/trePAR.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11907]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11011]
  
 
=== Additional information===
 
=== Additional information===
Line 54: Line 54:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:''' transports arabinose, and also xylose and galactose [http://www.ncbi.nlm.nih.gov/sites/entrez/9620981 PubMed]
+
* '''Catalyzed reaction/ biological activity:'''  
  
 
* '''Protein family:'''
 
* '''Protein family:'''
Line 74: Line 74:
 
* '''Interactions:'''
 
* '''Interactions:'''
  
−
* '''Localization:''' cell membrane (according to Swiss-Prot)
+
* '''Localization:'''
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''Structure:'''
+
* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=2OGG 2OGG] (effector binding domain)
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P96710 P96710]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P39796 P39796]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU33960]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU07820]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
Line 90: Line 90:
 
=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:'''  
+
* '''Operon:''' ''[[treP]]-[[treA]]-[[treR]]''
  
−
* '''[[Sigma factor]]:'''  
+
* '''[[Sigma factor]]:''' [[SigA]]
  
−
* '''Regulation:''' repressed by glucose ([[CcpA]]), induced by arabinose [http://www.ncbi.nlm.nih.gov/sites/entrez/9620981 PubMed]
+
* '''Regulation:''' repressed by glucose ([[CcpA]])   
−
** repressed in the absence of arabinose ([[AraR]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/10417639 PubMed]
 
  
 
* '''Regulatory mechanism:''' [[CcpA]]: transcription repression  
 
* '''Regulatory mechanism:''' [[CcpA]]: transcription repression  
−
** [[AraR]]:  transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/10417639 PubMed]
 
  
 
* '''Additional information:'''
 
* '''Additional information:'''
Line 122: Line 120:
 
=References=
 
=References=
  
−
<pubmed>10417639,9620981 9401028, </pubmed>
+
<pubmed>8755887, </pubmed>
−
# Krispin, O., and R. Allmansberger. (1998) The ''Bacillus subtilis'' AraE protein displays a broad substrate specificity for several different sugars. ''J. Bacteriol.'' '''180:''' 3250-3252. [http://www.ncbi.nlm.nih.gov/sites/entrez/9620981 PubMed]
+
 
−
# Sá-Nogueira I, Ramos SS. (1997) Cloning, functional analysis, and transcriptional regulation of the Bacillus subtilis araE gene involved in L-arabinose utilization. ''J Bacteriol. '' '''Dec;179(24):''' 7705-11. [http://www.ncbi.nlm.nih.gov/sites/entrez/9401028 PubMed]
+
# Schöck F, Dahl MK (1996) Expression of the tre operon of Bacillus subtilis 168 is regulated by the repressor TreR. ''J Bacteriol.'' '''Aug;178(15):''' 4576-81. [http://www.ncbi.nlm.nih.gov/sites/entrez/8755887 PubMed]
−
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]
 

Revision as of 18:36, 12 June 2009

  • Description: transcription repressor of the treP-treA-treR operon

Gene name treR
Synonyms yfxA
Essential no
Product transcription repressor
Function regulaation of trehalose utilization
Metabolic function and regulation of this protein in SubtiPathways:
Sugar catabolism
MW, pI 27 kDa, 6.82
Gene length, protein length 714 bp, 238 aa
Immediate neighbours treA, yfkO
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
TreR context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Locus tag: BSU07820

Phenotypes of a mutant

Database entries

  • DBTBS entry: [1]
  • SubtiList entry: [2]

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity:
  • Protein family:
  • Paralogous protein(s):

Extended information on the protein

  • Kinetic information:
  • Domains:
  • Modification:
  • Cofactor(s):
  • Effectors of protein activity:
  • Interactions:
  • Localization:

Database entries

  • Structure: 2OGG (effector binding domain)
  • KEGG entry: [3]
  • E.C. number:

Additional information

Expression and regulation

  • Regulation: repressed by glucose (CcpA)
  • Regulatory mechanism: CcpA: transcription repression
  • Additional information:

Biological materials

  • Mutant:
  • Expression vector:
  • lacZ fusion:
  • GFP fusion:
  • two-hybrid system:
  • Antibody:

Labs working on this gene/protein

Your additional remarks

References

F Schöck, M K Dahl
Expression of the tre operon of Bacillus subtilis 168 is regulated by the repressor TreR.
J Bacteriol: 1996, 178(15);4576-81
[PubMed:8755887] [WorldCat.org] [DOI] (P p)


  1. Schöck F, Dahl MK (1996) Expression of the tre operon of Bacillus subtilis 168 is regulated by the repressor TreR. J Bacteriol. Aug;178(15): 4576-81. PubMed
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