Difference between revisions of "Sandbox"

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* '''Description:''' small RNA <br/><br/>
+
* '''Description:''' carbamoyl-phosphate transferase-arginine subunit B) <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'''
−
|''bsrG''
+
|''carB''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''cpa ''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || small RNA
+
|style="background:#ABCDEF;" align="center"| '''Product''' || carbamoyl-phosphate transferase-arginine subunit B)
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
+
|style="background:#ABCDEF;" align="center"|'''Function''' || biosynthesis of arginine
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length''' ||  bp
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 112 kDa, 4.712  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yolA]]'', ''[[yokL]]''
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 3090 bp, 1030 aa
 
|-
 
|-
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/genE.txt    Gene sequence      (+200bp)  ]'''  
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[carA]]'', ''[[argF]]''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:bsrG_context.gif]]
+
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB12965&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 +
|-
 +
|-
 +
|-
 +
|colspan="2" | '''Genetic context''' <br/> [[Image:carB_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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<br/><br/>
 
<br/><br/>
  
−
<br/><br/><br/><br/><br/>
 
 
=The gene=
 
=The gene=
  
 
=== Basic information ===
 
=== Basic information ===
  
−
* '''Locus tag:'''
+
* '''Locus tag:''' BSU11240
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
Line 40: Line 43:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' no entry
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/argCJBD-carAB-argF.html]
  
−
* '''SubtiList entry:''' no entry
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10196]
−
 
−
* '''Structure:'''
 
  
 
=== Additional information===
 
=== Additional information===
  
  
 +
=The protein=
 +
 +
=== Basic information/ Evolution ===
 +
 +
* '''Catalyzed reaction/ biological activity:''' 2 ATP + L-glutamine + HCO<sub>3</sub><sup>-</sup> + H<sub>2</sub>O = 2 ADP + phosphate + L-glutamate + carbamoyl phosphate (according to Swiss-Prot)
 +
 +
* '''Protein family:''' carB family (according to Swiss-Prot)
 +
 +
* '''Paralogous protein(s):''' [[PyrAB]]
 +
 +
=== Extended information on the protein ===
 +
 +
* '''Kinetic information:'''
 +
 +
* '''Domains:'''
 +
 +
* '''Modification:'''
 +
 +
* '''Cofactor(s):'''
 +
 +
* '''Effectors of protein activity:'''
 +
 +
* '''Interactions:'''
 +
 +
* '''Localization:'''
 +
 +
=== Database entries ===
 +
 +
* '''Structure:'''
 +
 +
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P18185 P18185]
 +
 +
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU11240]
 +
 +
* '''E.C. number:''' [http://www.expasy.org/enzyme/6.3.5.5 6.3.5.5]
 +
 +
=== Additional information===
 +
 +
:* subject to Clp-dependent proteolysis upon glucose starvation [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+17981983 PubMed]
 
=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:'''  
+
* '''Operon:''' ''[[argC]]-[[argJ]]-[[argB]]-[[argD]]-[[carA]]-[[carB]]-[[argF]]''
  
−
* '''Sigma factor:'''  
+
* '''[[Sigma factor]]:''' [[SigA]]
  
−
* '''Regulation:'''  
+
* '''Regulation:''' repressed by casamino acids [http://www.ncbi.nlm.nih.gov/pubmed/12107147 PubMed], repressed by arginine ([[AhrC]])
  
−
* '''Regulatory mechanism:'''  
+
* '''Regulatory mechanism:''' [[AhrC]]: transcription repression
  
−
* '''Additional information:'''  
+
* '''Additional information:''' subject to Clp-dependent proteolysis upon glucose starvation [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+17981983 PubMed]
  
 
=Biological materials =
 
=Biological materials =
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* '''lacZ fusion:'''
 
* '''lacZ fusion:'''
  
 +
* '''GFP fusion:'''
 +
 +
* '''two-hybrid system:'''
  
−
=Labs working on this gene/RNA=
+
* '''Antibody:'''
  
−
Kouji Nakamura, Tsukuba, University, Japan
+
=Labs working on this gene/protein=
  
 
=Your additional remarks=
 
=Your additional remarks=
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=References=
 
=References=
  
−
<pubmed>18948176, </pubmed>
+
<pubmed>12107147, </pubmed>
−
# Saito S, Kakeshita H, Nakamura K (2009) Novel small RNA-encoding genes in the intergenic regions of ''Bacillus subtilis''. ''Gene'' '''428:''' 2-8. [http://www.ncbi.nlm.nih.gov/sites/entrez/18948176 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]
 +
# Gerth et al. (2008) Clp-dependent proteolysis down-regulates central metabolic pathways in glucose-starved Bacillus subtilis. J Bacteriol 190:321-331 [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+17981983 PubMed]
 +
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]

Revision as of 14:11, 8 June 2009

  • Description: carbamoyl-phosphate transferase-arginine subunit B)

Gene name carB
Synonyms cpa
Essential no
Product carbamoyl-phosphate transferase-arginine subunit B)
Function biosynthesis of arginine
MW, pI 112 kDa, 4.712
Gene length, protein length 3090 bp, 1030 aa
Immediate neighbours carA, argF
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
CarB context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Locus tag: BSU11240

Phenotypes of a mutant

Database entries

  • DBTBS entry: [1]
  • SubtiList entry: [2]

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity: 2 ATP + L-glutamine + HCO3- + H2O = 2 ADP + phosphate + L-glutamate + carbamoyl phosphate (according to Swiss-Prot)
  • Protein family: carB family (according to Swiss-Prot)
  • Paralogous protein(s): PyrAB

Extended information on the protein

  • Kinetic information:
  • Domains:
  • Modification:
  • Cofactor(s):
  • Effectors of protein activity:
  • Interactions:
  • Localization:

Database entries

  • Structure:
  • KEGG entry: [3]

Additional information

  • subject to Clp-dependent proteolysis upon glucose starvation PubMed

Expression and regulation

  • Regulation: repressed by casamino acids PubMed, repressed by arginine (AhrC)
  • Regulatory mechanism: AhrC: transcription repression
  • Additional information: subject to Clp-dependent proteolysis upon glucose starvation PubMed

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. Gerth et al. (2008) Clp-dependent proteolysis down-regulates central metabolic pathways in glucose-starved Bacillus subtilis. J Bacteriol 190:321-331 PubMed
  3. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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