Difference between revisions of "Sandbox"

From SubtiWiki
Jump to: navigation, search
Line 1: Line 1:
−
* '''Description:''' formation of 2-deoxy-5-keto-gluconic acid (4th reaction) <br/><br/>
+
* '''Description:''' L-arabinose permease <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'''
−
|''iolB''
+
|''araE''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yxdB ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yvbR ''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || formation of 2-deoxy-5-keto-gluconic acid (4th reaction)
+
|style="background:#ABCDEF;" align="center"| '''Product''' || L-arabinose permease
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || myo-inositol catabolism
+
|style="background:#ABCDEF;" align="center"|'''Function''' || uptake of arabinose, galactose and xylose
 
|-
 
|-
 
|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''' || 30 kDa, 4.77  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 50 kDa, 9.259  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 813 bp, 271 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1392 bp, 464 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[iolC]]'', ''[[iolA]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[cggR]]'', ''[[araR]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB16011&#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:CAB15401&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:iolB_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:araE_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>
 
|-
 
|-
Line 37: Line 37:
 
=== Basic information ===
 
=== Basic information ===
  
−
* '''Locus tag:''' BSU39750
+
* '''Locus tag:''' BSU33960
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
Line 43: Line 43:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/mmsA-iolBCDEF-idh-iolHI-fbaB.html]
+
* '''DBTBS entry:''' no entry
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11118]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11907]
  
 
=== Additional information===
 
=== Additional information===
Line 54: Line 54:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:''' 5-deoxy-glucuronic acid = 5-dehydro-2-deoxy-D-gluconic acid (according to Swiss-Prot)
+
* '''Catalyzed reaction/ biological activity:''' transports arabinose, and also xylose and galactose [http://www.ncbi.nlm.nih.gov/sites/entrez/9620981 PubMed]
  
−
* '''Protein family:''' isomerase iolB family (according to Swiss-Prot)
+
* '''Protein family:'''
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
Line 74: Line 74:
 
* '''Interactions:'''
 
* '''Interactions:'''
  
−
* '''Localization:'''
+
* '''Localization:''' cell membrane (according to Swiss-Prot)
  
 
=== Database entries ===
 
=== Database entries ===
Line 80: Line 80:
 
* '''Structure:'''
 
* '''Structure:'''
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P42413 P42413]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P96710 P96710]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU39750]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU33960]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
Line 90: Line 90:
 
=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''[[iolA]]-[[iolB]]-[[iolC]]-[[iolD]]-[[iolE]]-[[iolF]]-[[iolG]]-[[iolH]]-[[iolJ]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/9226270 PubMed]
+
* '''Operon:'''  
  
−
* '''[[Sigma factor]]:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/9226270 PubMed]
+
* '''[[Sigma factor]]:'''  
  
−
* '''Regulation:'''  
+
* '''Regulation:''' repressed by glucose ([[CcpA]]),  induced by arabinose [http://www.ncbi.nlm.nih.gov/sites/entrez/9620981 PubMed]
−
** repressed in the absence of inositol ([[IolR]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/9887260 PubMed]
+
** repressed in the absence of arabinose ([[AraR]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/10417639 PubMed]
−
** repressed by glucose ([[CcpA]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/10666464 PubMed]  
 
−
** induced by inositol ([[IolR]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/9226270 PubMed]
 
  
−
* '''Regulatory mechanism:'''  
+
* '''Regulatory mechanism:''' [[CcpA]]: transcription repression  
−
** [[IolR]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/9887260 PubMed]
+
** [[AraR]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/10417639 PubMed]
−
** [[CcpA]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/10666464 PubMed]
 
−
** [[IolR]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/9226270 PubMed]
 
  
 
* '''Additional information:'''
 
* '''Additional information:'''
Line 121: Line 117:
  
 
=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
−
 
−
* [[Yasutaro Fujita]], University of Fukuyama, Japan
 
−
* [[Ken-ichi Yoshida]], Kobe University, Japan
 
  
 
=Your additional remarks=
 
=Your additional remarks=
Line 129: Line 122:
 
=References=
 
=References=
  
−
<pubmed>9887260,18310071, </pubmed>
+
<pubmed>10417639,9620981 9401028, </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]
−
# Yoshida K, Yamaguchi M, Morinaga T, Kinehara M, Ikeuchi M, Ashida H, Fujita Y. (2008) myo-Inositol catabolism in Bacillus subtilis. ''J Biol Chem. '' ''' Apr 18;283(16):''' 10415-24. [http://www.ncbi.nlm.nih.gov/sites/entrez/18310071 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]
 +
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]

Revision as of 18:26, 12 June 2009

  • Description: L-arabinose permease

Gene name araE
Synonyms yvbR
Essential no
Product L-arabinose permease
Function uptake of arabinose, galactose and xylose
Metabolic function and regulation of this protein in SubtiPathways:
Sugar catabolism
MW, pI 50 kDa, 9.259
Gene length, protein length 1392 bp, 464 aa
Immediate neighbours cggR, araR
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
AraE context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Locus tag: BSU33960

Phenotypes of a mutant

Database entries

  • DBTBS entry: no entry
  • SubtiList entry: [1]

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity: transports arabinose, and also xylose and galactose PubMed
  • Protein family:
  • Paralogous protein(s):

Extended information on the protein

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

Database entries

  • Structure:
  • KEGG entry: [2]
  • E.C. number:

Additional information

Expression and regulation

  • Operon:
  • Regulation: repressed by glucose (CcpA), induced by arabinose PubMed
    • repressed in the absence of arabinose (AraR) PubMed
  • 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

  1. 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. PubMed
  2. 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. PubMed
  3. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
Retrieved from "http://134.76.20.203/wiki//index.php?title=Sandbox&oldid=92524"