Difference between revisions of "Sandbox"

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−
* '''Description:''' L-arabinose transport (sugar-binding protein) <br/><br/>
+
* '''Description:''' repressor of the arabinose utilization genes <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'''
−
|''araN''
+
|''araR''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yseC ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''araC, yvbS ''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || L-arabinose transport (sugar-binding protein))
+
|style="background:#ABCDEF;" align="center"| '''Product''' || transcriptional repressor (LacI family))
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || uptake of arabinose
+
|style="background:#ABCDEF;" align="center"|'''Function''' || regulation of arabinose utilization
 +
(araABDLMNPQ-abfA) and of the araE/araR genes
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 48 kDa, 8.555  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 43 kDa, 6.341  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1299 bp, 433 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1152 bp, 384 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[araP]]'', ''[[araM]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[araE]]'', ''[[yvbT]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB14835&#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:CAB15402&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|-
+
|colspan="2" | '''Genetic context''' <br/> [[Image:araR_context.gif]]
−
|-
 
−
|colspan="2" | '''Genetic context''' <br/> [[Image:araN_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:''' BSU28750
+
* '''Locus tag:''' BSU33970
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
Line 43: Line 42:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' no entry
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/araR.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11910]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11913]
  
 
=== Additional information===
 
=== Additional information===
Line 56: Line 55:
 
* '''Catalyzed reaction/ biological activity:'''  
 
* '''Catalyzed reaction/ biological activity:'''  
  
−
* '''Protein family:''' bacterial solute-binding protein 1 family (according to Swiss-Prot)
+
* '''Protein family:'''
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
 +
 +
=== Genes/ operons controlled by AraR ===
 +
 +
* '''Activated by AraR:'''
 +
* ''' Repressed by AraR:''' ''[[araA]]-[[araB]]-[[araD]]-[[araL]]-[[araM]]-[[araN]]-[[araP]]-[[araQ]]-[[abfA]]''
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
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* '''Interactions:'''
 
* '''Interactions:'''
  
−
* '''Localization:''' cell membrane (according to Swiss-Prot)
+
* '''Localization:''' cytoplasm (according to Swiss-Prot)
  
 
=== Database entries ===
 
=== Database entries ===
Line 80: Line 84:
 
* '''Structure:'''
 
* '''Structure:'''
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P94528 P94528]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P96711 P96711]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU28750]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU33970]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
Line 90: Line 94:
 
=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''[[araA]]-[[araB]]-[[araD]]-[[araL]]-[[araM]]-[[araN]]-[[araP]]-[[araQ]]-[[abfA]]''
+
* '''Operon:'''  
  
−
* '''[[Sigma factor]]:''' [[SigA]]
+
* '''[[Sigma factor]]:'''  
  
−
* '''Regulation:''' repressed by glucose ([[CcpA]])
+
* '''Regulation:'''  
  
−
* '''Regulatory mechanism:''' [[CcpA]]: transcription repression
+
* '''Regulatory mechanism:'''  
  
−
* '''Additional information:'''
+
* '''Additional information:'''  
  
 
=Biological materials =
 
=Biological materials =
Line 120: Line 124:
 
=References=
 
=References=
  
−
<pubmed>9084180, </pubmed>
+
<pubmed>10417639 9045819, </pubmed>
−
# Inácio JM, Costa C, de Sá-Nogueira I. (2003) Distinct molecular mechanisms involved in carbon catabolite repression of the arabinose regulon in Bacillus subtilis. ''Microbiology. '' '''Sep;149(Pt 9):''' 2345-55. [http://www.ncbi.nlm.nih.gov/sites/entrez/12949161 PubMed
+
# Mota LJ, Tavares P, Sá-Nogueira I. (1999) Mode of action of AraR, the key regulator of L-arabinose metabolism in Bacillus subtilis. ''Mol Microbiol.'' '''Aug;33(3):''' 476-89. [http://www.ncbi.nlm.nih.gov/sites/entrez/10417639 PubMed]
−
# Sa-Nogueira I.M.G., Nogueira T.V., Soares S., de Lencastre H. (1997) The Bacillus subtilis L-arabinose (ara) operon: nucleotide sequence, genetic organization and expression. ''Microbiology.'' '''Mar;143(Pt 3):''' 957-69. [http://www.ncbi.nlm.nih.gov/sites/entrez/9084180 PubMed]
+
# Sá-Nogueira I, Mota LJ. (1997) Negative regulation of L-arabinose metabolism in Bacillus subtilis: characterization of the araR (araC) gene. ''J Bacteriol. '' '''Mar;179(5):''' 1598-608. [http://www.ncbi.nlm.nih.gov/sites/entrez/9045819 PubMed]
−
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]
 

Revision as of 14:08, 8 June 2009

  • Description: repressor of the arabinose utilization genes

Gene name araR
Synonyms araC, yvbS
Essential no
Product transcriptional repressor (LacI family))
Function regulation of arabinose utilization

(araABDLMNPQ-abfA) and of the araE/araR genes

MW, pI 43 kDa, 6.341
Gene length, protein length 1152 bp, 384 aa
Immediate neighbours araE, yvbT
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
AraR context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Locus tag: BSU33970

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):

Genes/ operons controlled by AraR

Extended information on the protein

  • Kinetic information:
  • Domains:
  • Modification:
  • Cofactor(s):
  • Effectors of protein activity:
  • Interactions:
  • Localization: cytoplasm (according to Swiss-Prot)

Database entries

  • Structure:
  • KEGG entry: [3]
  • E.C. number:

Additional information

Expression and regulation

  • Operon:
  • Regulation:
  • Regulatory mechanism:
  • 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

L J Mota, P Tavares, I Sá-Nogueira
Mode of action of AraR, the key regulator of L-arabinose metabolism in Bacillus subtilis.
Mol Microbiol: 1999, 33(3);476-89
[PubMed:10417639] [WorldCat.org] [DOI] (P p)

I Sá-Nogueira, L J Mota
Negative regulation of L-arabinose metabolism in Bacillus subtilis: characterization of the araR (araC) gene.
J Bacteriol: 1997, 179(5);1598-608
[PubMed:9045819] [WorldCat.org] [DOI] (P p)

  1. Mota LJ, Tavares P, Sá-Nogueira I. (1999) Mode of action of AraR, the key regulator of L-arabinose metabolism in Bacillus subtilis. Mol Microbiol. Aug;33(3): 476-89. PubMed
  2. Sá-Nogueira I, Mota LJ. (1997) Negative regulation of L-arabinose metabolism in Bacillus subtilis: characterization of the araR (araC) gene. J Bacteriol. Mar;179(5): 1598-608. PubMed
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