Difference between revisions of "Sandbox"

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−
* '''Description:''' citrate synthase <br/><br/>
+
* '''Description:''' unknown <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'''
−
|''citZ''
+
|''ytvI''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''citA2 ''
+
|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''' || citrate synthase II
+
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || TCA cycle
+
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 41 kDa, 5.451  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 40 kDa, 9.374  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1116 bp, 372 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1113 bp, 371 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ytwI]], [[icd]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ytwI]]'', ''[[ytzA]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB14874&#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:CAB14876&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:citZ_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:ytvI_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 38: Line 38:
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
−
glutamate auxotrophy and a defect in sporulation [http://www.ncbi.nlm.nih.gov/pubmed/8045898 PubMed]
 
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/citZ-icd-mdh.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ytvI.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10855]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13930]
  
 
=== Additional information===
 
=== Additional information===
Line 53: Line 52:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:''' acetyl-CoA + oxaloacetate ---> citrate, the reaction is irreversible
+
* '''Catalyzed reaction/ biological activity:'''  
  
−
* '''Protein family:''' citrate synthase family
+
* '''Protein family:''' UPF0118 (perM) family
  
−
* '''Paralogous protein(s):''' [[MmgD]], [[CitA]]
+
* '''Paralogous protein(s):'''
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
Line 65: Line 64:
 
* '''Domains:'''  
 
* '''Domains:'''  
  
−
* '''Modification:''' phosphorylation on Ser-284 [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed]
+
* '''Modification:'''
  
 
* '''Cofactor(s):'''
 
* '''Cofactor(s):'''
  
−
* '''Effectors of protein activity:''' inhibited by ATP [http://www.ncbi.nlm.nih.gov/sites/entrez/4980242 PubMed]
+
* '''Effectors of protein activity:'''
  
 
* '''Interactions:'''
 
* '''Interactions:'''
  
−
* '''Localization:'''
+
* '''Localization:''' cell membrane (according to Swiss-Prot)
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=2C6X 2C6X]
+
* '''Structure:'''
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P39120 P39120]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/O34991 O34991]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU29140]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU29160]
  
−
* '''E.C. number:''' 4.1.3.7
+
* '''E.C. number:'''
  
 
=== Additional information===
 
=== Additional information===
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=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''[[citZ]]-[[icd]]-[[mdh]]''
+
* '''Operon:'''  
  
−
* '''Sigma factor:''' [[SigA]]
+
* '''[[Sigma factor]]:'''  
  
−
* '''Regulation:''' repressed by glucose (6.7-fold) ([[CcpA]]) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed],  catabolite repression ([[CcpA]]), repression by glucose + glutamate ([[CcpC]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/12100558 PubMed], repression under anaerobic conditions [http://www.ncbi.nlm.nih.gov/pubmed/9642180 PubMed]
+
* '''Regulation:'''  
  
−
* '''Regulatory mechanism:''' [[CcpA]]: transcription repression,  [[CcpA]]: transcription repression, [[CcpC]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/12100558 PubMed]
+
* '''Regulatory mechanism:'''  
  
−
* '''Additional information:'''
+
* '''Additional information:'''  
  
 
=Biological materials =
 
=Biological materials =
  
−
* '''Mutant:''' GP678 (erm), available in [[Stülke]] lab
+
* '''Mutant:'''
  
 
* '''Expression vector:'''
 
* '''Expression vector:'''
Line 111: Line 110:
 
* '''two-hybrid system:'''  
 
* '''two-hybrid system:'''  
  
−
* '''Antibody:''' available in [[Linc Sonenshein]] lab
+
* '''Antibody:'''
  
 
=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
−
 
−
[[Linc Sonenshein|Linc Sonenshein]], Tufts University, Boston, MA, USA [http://www.tufts.edu/sackler/microbiology/faculty/sonenshein/index.html Homepage]
 
−
 
−
[[Stülke|Jörg Stülke]], University of Göttingen, Germany
 
−
[http://wwwuser.gwdg.de/~genmibio/stuelke.html Homepage]
 
  
 
=Your additional remarks=
 
=Your additional remarks=
Line 124: Line 118:
 
=References=
 
=References=
  
−
# 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]
 
−
# Kim HJ, Roux A, Sonenshein AL (2002b) Direct and indirect roles of CcpA in regulation of ''Bacillus subtilis'' Krebs cycle genes. Mol Microbiol 45:179-190. [http://www.ncbi.nlm.nih.gov/sites/entrez/12100558 PubMed]
 
−
# Nakano MM, Zuber P, Sonenshein AL (1998) Anaerobic regulation of ''Bacillus subtilis'' Krebs cycle genes. ''J Bacteriol.'' '''180:''' 3304-3311. [http://www.ncbi.nlm.nih.gov/pubmed/9642180 PubMed]
 
−
# Jin S, Sonenshein AL  (1994) Identification of two distinct ''Bacillus subtilis'' citrate synthase genes ''J Bacteriol.'' '''176:''' 4669-4679. [http://www.ncbi.nlm.nih.gov/pubmed/8045898 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 08:57, 7 May 2009

  • Description: unknown

Gene name ytvI
Synonyms
Essential no
Product unknown
Function unknown
MW, pI 40 kDa, 9.374
Gene length, protein length 1113 bp, 371 aa
Immediate neighbours ytwI, ytzA
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
YtvI 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: UPF0118 (perM) family
  • 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: [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

Your additional remarks

References

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