Difference between revisions of "Sandbox"

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* '''Description:''' DNA topoisomerase I <br/><br/>
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* '''Description:''' succinyl-CoA synthetase (alpha subunit) <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'''
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|''topA''
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|''sucD''
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''topI ''
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|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"| '''Product''' || DNA topoisomerase I
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|style="background:#ABCDEF;" align="center"| '''Product''' || succinyl-CoA synthetase (alpha subunit)
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"|'''Function''' || replication
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|style="background:#ABCDEF;" align="center"|'''Function''' || TCA cycle 
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 78 kDa, 9.023  
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|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 31 kDa, 5.587  
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 2073 bp, 691 aa  
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|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 900 bp, 300 aa  
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[smf]]'', ''[[gid]]''
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|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[sucC]], [[smf]]''
 
|-
 
|-
 
|colspan="2" style="background:#FAF8CC;" align="center"|'''Hier soll was neues rein'''
 
|colspan="2" style="background:#FAF8CC;" align="center"|'''Hier soll was neues rein'''
 
|-
 
|-
−
|-
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|colspan="2" | '''Genetic context''' <br/> [[Image:sucD_context.gif]]
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|-
 
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|colspan="2" | '''Genetic context''' <br/> [[Image:topA_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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=== Database entries ===
 
=== Database entries ===
  
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* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/topA.html]
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* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/sucCD.html]
  
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* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11007]
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* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12681]
  
 
=== Additional information===
 
=== Additional information===
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* '''Protein family:'''
 
* '''Protein family:'''
  
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* '''Paralogous protein(s):''' [[TopB]], one of the two proteins has to be present for viability [http://www.ncbi.nlm.nih.gov/sites/entrez/17114254 PubMed]
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* '''Paralogous protein(s):'''
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
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* '''Domains:'''  
 
* '''Domains:'''  
  
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* '''Modification:'''
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* '''Modification:''' phosphorylation on (Ser-19 OR Thr-20) [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed]
  
 
* '''Cofactor(s):'''
 
* '''Cofactor(s):'''
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=== Database entries ===
 
=== Database entries ===
  
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* '''Structure:'''
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* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1JKJ 1JKJ] (E. coli)
  
 
* '''Swiss prot entry:'''
 
* '''Swiss prot entry:'''
  
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* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU16120]
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* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU16100]
  
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* '''E.C. number:'''
+
* '''E.C. number:''' 6.2.1.5
  
 
=== Additional information===
 
=== Additional information===
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=Expression and regulation=
 
=Expression and regulation=
  
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* '''Operon:'''  
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* '''Operon:''' ''[[sucC]]''-''[[SucD]]''
  
−
* '''[[Sigma factor]]:'''  
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* '''Sigma factor:'''  
  
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* '''Regulation:'''  
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* '''Regulation:''' repressed by glucose (2.4-fold) ([[CcpA]]) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed] 
  
−
* '''Regulatory mechanism:'''  
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* '''Regulatory mechanism:''' [[CcpA]]: transcription repression
  
−
* '''Additional information:'''  
+
* '''Additional information:'''
  
 
=Biological materials =
 
=Biological materials =
  
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* '''Mutant:'''
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* '''Mutant:''' GP720 (spc), available in [[Stülke]] lab
  
 
* '''Expression vector:'''
 
* '''Expression vector:'''
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=References=
 
=References=
  
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# Thomaides, H. B., Davison, E. J., Burston, L., Johnson, H., Brown, D. R., Hunt, A. C., Errington, J., and Czaplewski, L. (2007) Essential bacterial functions encoded by gene pairs. J Bacteriol 189, 591-602. [http://www.ncbi.nlm.nih.gov/sites/entrez/17114254 PubMed]
+
# Blencke et al. (2003) Transcriptional profiling of gene expression in response to glucose in ''Bacillus subtilis'': regulation of the central metabolic pathways. ''Metab Eng.'' '''5:''' 133-149 [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]# Macek et al. (2007) The serine/ threonine/ tyrosine phosphoproteome of the model  bacterium ''Bacillus subtilis''. Mol. Cell. Proteomics 6: 697-707  [http://www.ncbi.nlm.nih.gov/pubmed/17218307 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 19:50, 15 April 2009

  • Description: succinyl-CoA synthetase (alpha subunit)

Gene name sucD
Synonyms
Essential no
Product succinyl-CoA synthetase (alpha subunit)
Function TCA cycle
MW, pI 31 kDa, 5.587
Gene length, protein length 900 bp, 300 aa
Immediate neighbours sucC, smf
Hier soll was neues rein
Genetic context
SucD 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: phosphorylation on (Ser-19 OR Thr-20) PubMed
  • Cofactor(s):
  • Effectors of protein activity:
  • Interactions:
  • Localization:

Database entries

  • Structure: 1JKJ (E. coli)
  • Swiss prot entry:
  • KEGG entry: [3]
  • E.C. number: 6.2.1.5

Additional information

Expression and regulation

  • Sigma factor:
  • Regulation: repressed by glucose (2.4-fold) (CcpA) PubMed
  • Regulatory mechanism: CcpA: transcription repression
  • Additional information:

Biological materials

  • Mutant: GP720 (spc), available in Stülke lab
  • Expression vector:
  • lacZ fusion:
  • GFP fusion:
  • two-hybrid system:
  • Antibody:

Labs working on this gene/protein

Your additional remarks

References

  1. Blencke et al. (2003) Transcriptional profiling of gene expression in response to glucose in Bacillus subtilis: regulation of the central metabolic pathways. Metab Eng. 5: 133-149 PubMed# Macek et al. (2007) The serine/ threonine/ tyrosine phosphoproteome of the model bacterium Bacillus subtilis. Mol. Cell. Proteomics 6: 697-707 PubMed
  2. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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