Difference between revisions of "Sandbox"

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* '''Description:''' L-arabinose permease <br/><br/>
+
* '''Description:''' L-arabinose transport (sugar-binding protein) <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''
+
|''araN''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yvbR ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yseC ''
 
|-
 
|-
 
|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''' || L-arabinose transport (sugar-binding protein))
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || uptake of arabinose, galactose and xylose
+
|style="background:#ABCDEF;" align="center"|'''Function''' || uptake of arabinose
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 50 kDa, 9.259  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 48 kDa, 8.555  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1392 bp, 464 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1299 bp, 433 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[cggR]]'', ''[[araR]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[araP]]'', ''[[araM]]''
 
|-
 
|-
−
|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:CAB14835&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:araE_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:''' BSU33960
+
* '''Locus tag:''' BSU28750
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
Line 43: Line 45:
 
* '''DBTBS entry:''' no entry
 
* '''DBTBS entry:''' no entry
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11907]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11910]
  
 
=== Additional information===
 
=== Additional information===
Line 52: 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:''' bacterial solute-binding protein 1 family (according to Swiss-Prot)
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
Line 78: Line 80:
 
* '''Structure:'''
 
* '''Structure:'''
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P96710 P96710]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P94528 P94528]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU33960]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU28750]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
Line 88: Line 90:
 
=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:'''  
+
* '''Operon:''' ''[[araA]]-[[araB]]-[[araD]]-[[araL]]-[[araM]]-[[araN]]-[[araP]]-[[araQ]]-[[abfA]]''
  
−
* '''[[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]])
  
 
* '''Regulatory mechanism:''' [[CcpA]]: transcription repression  
 
* '''Regulatory mechanism:''' [[CcpA]]: transcription repression  
Line 118: Line 120:
 
=References=
 
=References=
  
−
<pubmed>9620981 9401028, </pubmed>
+
<pubmed>9084180, </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]
+
# 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
−
# 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]
+
# 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]
 
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]
 
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]

Revision as of 13:08, 8 June 2009

  • Description: L-arabinose transport (sugar-binding protein)

Gene name araN
Synonyms yseC
Essential no
Product L-arabinose transport (sugar-binding protein))
Function uptake of arabinose
MW, pI 48 kDa, 8.555
Gene length, protein length 1299 bp, 433 aa
Immediate neighbours araP, araM
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
AraN context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Locus tag: BSU28750

Phenotypes of a mutant

Database entries

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

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity:
  • Protein family: bacterial solute-binding protein 1 family (according to Swiss-Prot)
  • 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

  • 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

Isabel S-Nogueira, Teresa V Nogueira, Snia Soares, Hermnia de Lencastre
The Bacillus subtilis L-arabinose (ara) operon: nucleotide sequence, genetic organization and expression.
Microbiology (Reading): 1997, 143 ( Pt 3);957-969
[PubMed:9084180] [WorldCat.org] [DOI] (P p)

  1. 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
  2. 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. PubMed
  3. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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