Difference between revisions of "Sandbox"

From SubtiWiki
Jump to: navigation, search
Line 1: Line 1:
−
* '''Description:''' phosphoenolpyruvate carboxykinase <br/><br/>
+
* '''Description:''' bacillopeptidase F <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'''
−
|''pckA''
+
|''bpr''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ppc''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''bpf ''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
+
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || phosphoenolpyruvate carboxykinase
+
|style="background:#ABCDEF;" align="center"| '''Product''' || bacillopeptidase F
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || synthesis of phosphoenolpyruvate
+
|style="background:#ABCDEF;" align="center"|'''Function''' || protein degradation
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 58,1 kDa, 5.12
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 154 kDa, 4.976 
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1581 bp, 527 amino acids
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 4299 bp, 1433 aa
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[metK]]'', ''[[ytmB]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ftsZ]]'', ''[[spoIIGA]]''
 
|-
 
|-
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/pckA_nucleotide.txt    Gene sequence      (+200bp) ]'''  
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/bpr_nucleotide.txt    Gene sequence      (+200bp)   ]'''  
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/pckA_protein.txt Protein sequence]'''
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/bpr_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" style="background:#FAF8CC;color:#FF0000" align="center" | '''Caution: The sequence for this gene in SubtiList contains errors
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:pckA_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:bpr_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 33: Line 33:
  
 
<br/><br/>
 
<br/><br/>
−
 
  
 
=The gene=
 
=The gene=
Line 39: Line 38:
 
=== Basic information ===
 
=== Basic information ===
  
−
* '''Coordinates:''' 3128579 - 3130159
+
* '''Coordinates:'''
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
Line 45: Line 44:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/pckA.html]
+
* '''DBTBS entry:''' no entry
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11841]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10233]
  
 
=== Additional information===
 
=== Additional information===
 +
  
 
=The protein=
 
=The protein=
Line 55: Line 55:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:''' ATP + oxaloacetate = ADP + phosphoenolpyruvate + CO(2)
+
* '''Catalyzed reaction/ biological activity:'''  
  
−
* '''Protein family:''' phosphoenolpyruvate carboxykinase [ATP] family
+
* '''Protein family:'''
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
Line 66: Line 66:
  
 
* '''Domains:'''  
 
* '''Domains:'''  
−
** Nucleotide binding Domain (233–240)
 
  
 
* '''Modification:'''
 
* '''Modification:'''
Line 76: Line 75:
 
* '''Interactions:'''
 
* '''Interactions:'''
  
−
* '''Localization:''' cytoplasm
+
* '''Localization:'''
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=2PXZ 2PXZ] (''E.coli'')
+
* '''Structure:'''
  
−
* '''Swiss prot entry:''' [http://www.expasy.ch/cgi-bin/sprot-search-ac?P54418]
+
* '''Swiss prot entry:'''
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU30560]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU15300]
  
−
* '''E.C. number:''' [http://www.expasy.ch/cgi-bin/get-enzyme-entry?4.1.1.49]
+
* '''E.C. number:'''
  
 
=== Additional information===
 
=== Additional information===
−
 
  
 
=Expression and regulation=
 
=Expression and regulation=
Line 95: Line 93:
 
* '''Operon:'''  
 
* '''Operon:'''  
  
−
* '''Sigma factor:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+15720552 PubMed]
+
* '''Sigma factor:'''  
  
−
* '''Regulation:''' repressed by glucose (7-fold) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed], repressed (35-times) Glc, repressor [[CcpN]] [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+15720552 PubMed]
+
* '''Regulation:''' repressed by glucose (7.7-fold) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]   
  
−
* '''Regulatory mechanism:''' transcription repression
+
* '''Regulatory mechanism:'''  
  
−
* '''Additional information:'''
+
* '''Additional information:'''  
  
 
=Biological materials =
 
=Biological materials =
Line 108: Line 106:
  
 
* '''Expression vector:'''
 
* '''Expression vector:'''
−
+
       
 
* '''lacZ fusion:'''
 
* '''lacZ fusion:'''
  
 
* '''GFP fusion:'''
 
* '''GFP fusion:'''
 +
 +
* '''two-hybrid system:'''
  
 
* '''Antibody:'''
 
* '''Antibody:'''
  
 
=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
−
 
−
[[Stephane Aymerich |Stephane Aymerich]], Microbiology and Molecular Genetics, INRA Paris-Grignon, France
 
  
 
=Your additional remarks=
 
=Your additional remarks=
Line 124: Line 122:
  
 
# 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]
 
# 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]
−
# Servant et al. (2005) CcpN (YqzB), a novel regulator for CcpA-independent catabolite repression of ''Bacillus subtilis'' gluconeogenic genes. Mol. Microbiol. 55: 1435-1451. [http://www.ncbi.nlm.nih.gov/sites/entrez/15720552 PubMed]
+
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]
−
# Tännler et al. (2008) CcpN controls central carbon fluxes in ''Bacillus subtilis''. J. Bacteriol. 190: 6178-6187. [http://www.ncbi.nlm.nih.gov/sites/entrez/18586936 PubMed]
 

Revision as of 02:07, 3 April 2009

  • Description: bacillopeptidase F

Gene name bpr
Synonyms bpf
Essential no
Product bacillopeptidase F
Function protein degradation
MW, pI 154 kDa, 4.976
Gene length, protein length 4299 bp, 1433 aa
Immediate neighbours ftsZ, spoIIGA
Gene sequence (+200bp) Protein sequence
Caution: The sequence for this gene in SubtiList contains errors
Genetic context
Bpr context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Coordinates:

Phenotypes of a mutant

Database entries

  • DBTBS entry: no entry
  • SubtiList entry: [1]

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: [2]
  • E.C. number:

Additional information

Expression and regulation

  • Operon:
  • Sigma factor:
  • Regulation: repressed by glucose (7.7-fold) 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. 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
  2. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
Retrieved from "http://subtiwiki.uni-goettingen.de/wiki//index.php?title=Sandbox&oldid=47016"