Difference between revisions of "Sandbox"

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−
* '''Description:''' transcriptional repressor of the gluconate operon <br/><br/>
+
* '''Description:''' general stress 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'''
−
|''gntR''
+
|''gsiB''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
 
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
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|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || transcriptional repressor of the gluconate operon
+
|style="background:#ABCDEF;" align="center"| '''Product''' || general stress protein
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || regulation of gluconate utilization
+
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 28 kDa, 5.26  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 13 kDa, 5.145  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 729 bp, 243 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 369 bp, 123 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yxaA]]'', ''[[gntK]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ydbA]]'', ''[[ydbB]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB16042&#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:CAB12247&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:gntR_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:gsiB_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:''' BSU40050
+
* '''Locus tag:''' BSU04400
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
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=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/gntRKPZ.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/gsiB.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10648]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10826]
  
 
=== Additional information===
 
=== Additional information===
Line 68: Line 68:
 
* '''Cofactor(s):'''
 
* '''Cofactor(s):'''
  
−
* '''Effectors of protein activity:''' gluconate acts as molecular inducer
+
* '''Effectors of protein activity:'''
  
 
* '''Interactions:'''
 
* '''Interactions:'''
Line 78: Line 78:
 
* '''Structure:'''
 
* '''Structure:'''
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P10585 P10585]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P26907 P26907]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU40050]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU04400]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
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=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''[[gntR]]-[[gntK]]-[[gntP]]-[[gntZ]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/10746760 PubMed1][http://www.ncbi.nlm.nih.gov/sites/entrez/3020045 PubMed2]
+
* '''Operon:''' ''gsiB''
  
−
* '''[[Sigma factor]]:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/3020045 PubMed]
+
* '''[[Sigma factor]]:''' [[SigB]], [[SigI]] [http://www.ncbi.nlm.nih.gov/sites/entrez/11157964 PubMed]
  
−
* '''Regulation:'''  
+
* '''Regulation:'''  induced by stress ([[SigB]]) [http://www.ncbi.nlm.nih.gov/pubmed/11544224 PubMed]
−
** induced by gluconate ([[GntR]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/3020045 PubMed]
 
−
** repressed by glucose ([[CcpA]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/8370661 PubMed]
 
  
 
* '''Regulatory mechanism:'''  
 
* '''Regulatory mechanism:'''  
−
** [[GntR]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/3020045 PubMed]
 
−
** [[CcpA]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/10666464 PubMed]
 
  
−
* '''Additional information:'''
+
* '''Additional information:''' the mRNA is very stable (half-life > 15 min) [http://www.ncbi.nlm.nih.gov/sites/entrez/12884008 PubMed]
  
 
=Biological materials =
 
=Biological materials =
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=References=
 
=References=
  
−
<pubmed>7476858 3020045 1659648, </pubmed>
+
<pubmed>11544224, </pubmed>
−
# Yoshida K, Miwa Y, Ohmori H, Fujita Y. (1995) Analysis of an insertional operator mutation (gntOi) that affects the expression level of the Bacillus subtilis gnt operon, and characterization of gntOi suppressor mutations. ''Mol Gen Genet.'' '''Sep 20;248(5):''' 583-91. [http://www.ncbi.nlm.nih.gov/sites/entrez/7476858 PubMed]
+
# Petersohn et al. (2001) Global Analysis of the General Stress Response of ''Bacillus subtilis''. ''J Bacteriol.'' '''183:''' 5617-5631 [http://www.ncbi.nlm.nih.gov/pubmed/11544224 PubMed]
−
# Fujita Y, Fujita T, Miwa Y, Nihashi J, Aratani Y. (1986) Organization and transcription of the gluconate operon, gnt, of Bacillus subtilis. ''J Biol Chem.'' '''Oct 15;261(29):''' 13744-53. [http://www.ncbi.nlm.nih.gov/sites/entrez/3020045 PubMed]
+
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]
−
# Reizer A., Deutscher J., Saier M.H. Jr., Reizer J. (1991) Analysis of the gluconate (gnt) operon of Bacillus subtilis. ''Mol. Microbiol.'' '''5:''' 1081-1089. [http://www.ncbi.nlm.nih.gov/sites/entrez/1659648 PubMed]
 

Revision as of 14:19, 8 June 2009

  • Description: general stress protein

Gene name gsiB
Synonyms
Essential no
Product general stress protein
Function unknown
MW, pI 13 kDa, 5.145
Gene length, protein length 369 bp, 123 aa
Immediate neighbours ydbA, ydbB
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
GsiB context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Locus tag: BSU04400

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

Additional information

Expression and regulation

  • Operon: gsiB
  • Regulatory mechanism:
  • Additional information: the mRNA is very stable (half-life > 15 min) PubMed

Biological materials

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

Labs working on this gene/protein

Your additional remarks

References

A Petersohn, M Brigulla, S Haas, J D Hoheisel, U Völker, M Hecker
Global analysis of the general stress response of Bacillus subtilis.
J Bacteriol: 2001, 183(19);5617-31
[PubMed:11544224] [WorldCat.org] [DOI] (P p)

  1. Petersohn et al. (2001) Global Analysis of the General Stress Response of Bacillus subtilis. J Bacteriol. 183: 5617-5631 PubMed
  2. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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