Difference between revisions of "Sandbox"

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−
* '''Description:''' antilisterial bacteriocin (subtilosin) production <br/><br/>
+
* '''Description:''' ornithine carbamoyltransferase <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'''
−
|''albD''
+
|''argF''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ywhP ''
+
|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''' || unknown
+
|style="background:#ABCDEF;" align="center"| '''Product''' || ornithine carbamoyltransferase
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || antilisterial bacteriocin (subtilosin) production
+
|style="background:#ABCDEF;" align="center"|'''Function''' || biosynthesis of arginine
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 49 kDa, 10.119  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 34 kDa, 4.965  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1308 bp, 436 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 957 bp, 319 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[albC]]'', ''[[albE]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[carB]]'', ''[[yjzC]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB15767&#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:CAB12966&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:albD_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:argF_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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=== Basic information ===
 
=== Basic information ===
  
−
* '''Locus tag:''' BSU37400
+
* '''Locus tag:''' BSU11250
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
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=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/sboAX-albABCDEFG.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/argCJBD-carAB-argF.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12468]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10197]
  
 
=== Additional information===
 
=== Additional information===
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=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:'''  
+
* '''Catalyzed reaction/ biological activity:''' Carbamoyl phosphate + L-ornithine = phosphate + L-citrulline (according to Swiss-Prot)
  
−
* '''Protein family:'''
+
* '''Protein family:''' ATCase/OTCase family (according to Swiss-Prot)
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
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* '''Interactions:'''
 
* '''Interactions:'''
  
−
* '''Localization:''' cell membrane (according to Swiss-Prot)
+
* '''Localization:''' cytoplasm (according to Swiss-Prot)
  
 
=== Database entries ===
 
=== Database entries ===
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* '''Structure:'''
 
* '''Structure:'''
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P71008 P71008]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P18186 P18186]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU37400]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU11250]
  
−
* '''E.C. number:'''
+
* '''E.C. number:''' [http://www.expasy.org/enzyme/2.1.3.3 2.1.3.3]
  
 
=== Additional information===
 
=== Additional information===
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=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''[[sboA]]-[[sboX]]-[[albA]]-[[albB]]-[[albC]]-[[albD]]-[[albE]]-[[albF]]-[[albG]]''
+
* '''Operon:''' ''[[argC]]-[[argJ]]-[[argB]]-[[argD]]-[[carA]]-[[carB]]-[[argF]]''
  
−
* '''[[Sigma factor]]:''' [[SigA]]
+
* '''[[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:'''
Line 118: Line 118:
 
=References=
 
=References=
  
 +
# 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]
 
# 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 17:21, 7 June 2009

  • Description: ornithine carbamoyltransferase

Gene name argF
Synonyms
Essential no
Product ornithine carbamoyltransferase
Function biosynthesis of arginine
MW, pI 34 kDa, 4.965
Gene length, protein length 957 bp, 319 aa
Immediate neighbours carB, yjzC
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
ArgF context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Locus tag: BSU11250

Phenotypes of a mutant

Database entries

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

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity: Carbamoyl phosphate + L-ornithine = phosphate + L-citrulline (according to Swiss-Prot)
  • Protein family: ATCase/OTCase family (according to Swiss-Prot)
  • Paralogous protein(s):

Extended information on the protein

  • Kinetic information:
  • Domains:
  • Modification:
  • Cofactor(s):
  • Effectors of protein activity:
  • Interactions:
  • Localization: cytoplasm (according to Swiss-Prot)

Database entries

  • Structure:
  • KEGG entry: [3]

Additional information

Expression and regulation

  • Regulation: repressed by casamino acids PubMed , repressed by arginine (AhrC)
  • Regulatory mechanism: AhrC: transcription repression
  • 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. 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. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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