Difference between revisions of "Sandbox"

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* '''Description:''' transcriptional regulator of a subset of the SigB general stress regulon <br/><br/>
+
* '''Description:''' write here <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'''
−
|''mgsR ''
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|''sdpC''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yqgZ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yvaY ''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || transcriptional regulator
+
|style="background:#ABCDEF;" align="center"| '''Product''' ||  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || controls a subset of general stress genes
+
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 14 kDa, 9.28  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 22 kDa, 9.611  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 378 bp, 126 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 609 bp, 203 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[trnSL-Gln1]]'', ''[[yqgY]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[sdpB]]'', ''[[sdpI]]''
 
|-
 
|-
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/yqgZ_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/yvaY_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/yqgZ_protein.txt Protein sequence]'''
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/yvaY_protein.txt Protein sequence]'''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;color:#FF0000" align="center" | '''Caution: The sequence for this gene in SubtiList contains errors
+
|colspan="2" | '''Genetic context''' <br/> [[Image:yvaY_context.gif]]
−
|-
 
−
|colspan="2" | '''Genetic context''' <br/> [[Image:yqgZ_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 44: Line 42:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yqgZ.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/sdp.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11693]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG14076]
  
 
=== Additional information===
 
=== Additional information===
Line 55: Line 53:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:''' exerts a positive or negative effect on the expression of 53 or 18 stress genes, respectively [http://www.ncbi.nlm.nih.gov/sites/entrez/18643936 PubMed]
+
* '''Catalyzed reaction/ biological activity:'''  
  
−
* '''Protein family:''' Arsenate Reductase (ArsC) family, Spx subfamily
+
* '''Protein family:'''
  
−
* '''Paralogous protein(s):''' [[Spx]]
+
* '''Paralogous protein(s):'''
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
Line 83: Line 81:
 
* '''Swiss prot entry:'''
 
* '''Swiss prot entry:'''
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU24770]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU33770]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
Line 93: Line 91:
 
* '''Operon:'''  
 
* '''Operon:'''  
  
−
* '''Sigma factor:''' [[SigB]] [http://www.ncbi.nlm.nih.gov/sites/entrez/18643936 PubMed]
+
* '''Sigma factor:'''  
  
−
* '''Regulation:''' repressed by Casamino Acids [http://www.ncbi.nlm.nih.gov/pubmed/12107147 PubMed] ,  induced by stress ([[SigB]]) [http://www.ncbi.nlm.nih.gov/pubmed/15805528 PubMed], expressed under stress conditions [http://www.ncbi.nlm.nih.gov/sites/entrez/18643936 PubMed]
+
* '''Regulation:''' repressed by Casamino Acids [http://www.ncbi.nlm.nih.gov/pubmed/12107147 PubMed]
  
 
* '''Regulatory mechanism:'''  
 
* '''Regulatory mechanism:'''  
  
−
* '''Additional information:'''
+
* '''Additional information:'''  
  
 
=Biological materials =
 
=Biological materials =
Line 122: Line 120:
  
 
# M&#228;der et al. (2002) Transcriptome and Proteome Analysis of ''Bacillus subtilis'' Gene Expression Modulated by Amino Acid Availability. ''J. Bacteriol'' '''184:''' 1844288-4295 [http://www.ncbi.nlm.nih.gov/pubmed/12107147 PubMed]
 
# M&#228;der et al. (2002) Transcriptome and Proteome Analysis of ''Bacillus subtilis'' Gene Expression Modulated by Amino Acid Availability. ''J. Bacteriol'' '''184:''' 1844288-4295 [http://www.ncbi.nlm.nih.gov/pubmed/12107147 PubMed]
−
# H&ouml;per et al. (2005) Comprehensive Characterization of the Contribution of Individual [[SigB]]-Dependent General Stress Genes to Stress Resistance of ''Bacillus subtilis''. J. Bact. '''187:''' 2810-2826  [http://www.ncbi.nlm.nih.gov/pubmed/15805528 PubMed]
 
−
# Reder et al. (2008) The Spx paralogue MgsR (YqgZ) controls a subregulon within the general stress response of ''Bacillus subtilis''. ''Mol. Microbiol.'' '''69:''' 1104-1120. [http://www.ncbi.nlm.nih.gov/sites/entrez/18643936 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 11:16, 31 March 2009

  • Description: write here

Gene name sdpC
Synonyms yvaY
Essential no
Product
Function unknown
MW, pI 22 kDa, 9.611
Gene length, protein length 609 bp, 203 aa
Immediate neighbours sdpB, sdpI
Gene sequence (+200bp) Protein sequence
Genetic context
YvaY context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Coordinates:

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

Additional information

Expression and regulation

  • Operon:
  • Sigma factor:
  • Regulation: repressed by Casamino Acids PubMed
  • 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

  1. Mäder et al. (2002) Transcriptome and Proteome Analysis of Bacillus subtilis Gene Expression Modulated by Amino Acid Availability. J. Bacteriol 184: 1844288-4295 PubMed
  2. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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