Difference between revisions of "Sandbox"

From SubtiWiki
Jump to: navigation, search
Line 1: Line 1:
−
* '''Description:''' succinate dehydrogenase (flavoprotein subunit) <br/><br/>
+
* '''Description:''' transcriptional regulator required for the expression of SigK-dependent late spore coat 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'''
−
|''sdhA''
+
|''gerE''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''citF ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || succinate dehydrogenase (flavoprotein subunit)  
+
|style="background:#ABCDEF;" align="center"| '''Product''' || transcriptional regulator (LuxR-FixJ family)
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || TCA cycle
+
|style="background:#ABCDEF;" align="center"|'''Function''' || regulation of SigK-dependent gene expression
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 65 kDa, 5.714  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 8 kDa, 9.635  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1758 bp, 586 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 222 bp, 74 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[sdhC]], [[sdhB]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ysmB]]'', ''[[ysmA]]''
 
|-
 
|-
 
|colspan="2" style="background:#FAF8CC;" align="center"|'''Hier soll was neues rein'''
 
|colspan="2" style="background:#FAF8CC;" align="center"|'''Hier soll was neues rein'''
Line 24: Line 24:
 
|-
 
|-
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:sdhA_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:gerE_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 43: Line 43:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/sdhCAB.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/gerE.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10352]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10355]
  
 
=== Additional information===
 
=== Additional information===
Line 56: Line 56:
 
* '''Catalyzed reaction/ biological activity:'''  
 
* '''Catalyzed reaction/ biological activity:'''  
  
−
* '''Protein family:'''
+
* '''Protein family:''' LuxR-FixJ family of transcription regulators
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
 +
 +
=== Genes controlled by GerE ===
 +
 +
''[[lipC]],'' ''[[surC]]''
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
Line 66: Line 70:
 
* '''Domains:'''  
 
* '''Domains:'''  
  
−
* '''Modification:''' phosphorylated [http://www.ncbi.nlm.nih.gov/pubmed/16493705 PubMed], [http://www.ncbi.nlm.nih.gov/pubmed/17726680 PubMed]
+
* '''Modification:'''
  
 
* '''Cofactor(s):'''
 
* '''Cofactor(s):'''
Line 74: Line 78:
 
* '''Interactions:'''
 
* '''Interactions:'''
  
−
* '''Localization:''' membrane protein [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]
+
* '''Localization:'''
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1NEK 1NEK] (''E. coli'')
+
* '''Structure:'''
  
 
* '''Swiss prot entry:'''
 
* '''Swiss prot entry:'''
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU28440]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU28410]
  
−
* '''E.C. number:''' 1.3.99.1
+
* '''E.C. number:'''
  
 
=== Additional information===
 
=== Additional information===
Line 90: Line 94:
 
=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''[[sdhC]]''-''[[sdhA]]''-''[[sdhB]]''
+
* '''Operon:'''  
  
−
* '''[[Sigma factor]]:''' [[SigA]]  
+
* '''[[Sigma factor]]:''' [[SigK]]
  
−
* '''Regulation:''' constitutive
+
* '''Regulation:'''  
  
 
* '''Regulatory mechanism:'''  
 
* '''Regulatory mechanism:'''  
Line 102: Line 106:
 
=Biological materials =
 
=Biological materials =
  
−
* '''Mutant:''' GP743 (''sdhCA'', cat), available in [[Stülke]] lab
+
* '''Mutant:'''
  
 
* '''Expression vector:'''
 
* '''Expression vector:'''
Line 115: Line 119:
  
 
=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
 +
 +
[[Arthur Aronson]], Purdue University, West Lafayette, USA [http://wwwdev.gradschool.purdue.edu/PULSe/faculty.cfm?fid=5&range=0 homepage]
  
 
=Your additional remarks=
 
=Your additional remarks=
Line 120: Line 126:
 
=References=
 
=References=
  
−
# Eymann et al. (2007) Dynamics of protein phosphorylation on Ser/Thr/Tyr in ''Bacillus subtilis''. ''Proteomics'' '''7:''' 3509-3526. [http://www.ncbi.nlm.nih.gov/pubmed/17726680 PubMed]
+
# Crater DL, Moran CP Jr. (2001) Identification of a DNA binding region in GerE from Bacillus subtilis. ''J Bacteriol.'' '''Jul;183(14):''' 4183-9. [http://www.ncbi.nlm.nih.gov/sites/entrez/11418558 PubMed]
−
# Hahne et al. (2008) From complementarity to comprehensiveness - targeting the membrane proteome of growing ''Bacillus subtilis'' by divergent approaches. Proteomics '''8:''' 4123-4136 [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]# Eymann et al. (2007) Dynamics of protein phosphorylation on Ser/Thr/Tyr in ''Bacillus subtilis''. Proteomics 7: 3509-3526. [http://www.ncbi.nlm.nih.gov/pubmed/17726680 PubMed]
 
−
# Levine et al. (2006) Analysis of the dynamic ''Bacillus subtilis'' Ser/Thr/Tyr phosphoproteome implicated in a wide variety of cellular processes. Proteomics 6, 2157-2173. [http://www.ncbi.nlm.nih.gov/pubmed/16493705 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 15:06, 15 April 2009

  • Description: transcriptional regulator required for the expression of SigK-dependent late spore coat genes

Gene name gerE
Synonyms
Essential no
Product transcriptional regulator (LuxR-FixJ family)
Function regulation of SigK-dependent gene expression
MW, pI 8 kDa, 9.635
Gene length, protein length 222 bp, 74 aa
Immediate neighbours ysmB, ysmA
Hier soll was neues rein
Genetic context
GerE 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: LuxR-FixJ family of transcription regulators
  • Paralogous protein(s):

Genes controlled by GerE

lipC, surC

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:
  • Regulation:
  • Regulatory mechanism:
  • Additional information:

Biological materials

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

Labs working on this gene/protein

Arthur Aronson, Purdue University, West Lafayette, USA homepage

Your additional remarks

References

  1. Crater DL, Moran CP Jr. (2001) Identification of a DNA binding region in GerE from Bacillus subtilis. J Bacteriol. Jul;183(14): 4183-9. PubMed
  2. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
Retrieved from "http://subtiwiki.uni-goettingen.de/wiki//index.php?title=Sandbox&oldid=53511"