Difference between revisions of "Sandbox"

From SubtiWiki
Jump to: navigation, search
Line 1: Line 1:
−
* '''Description:''' repressor of the arabinose utilization genes <br/><br/>
+
* '''Description:''' N-acetyl-g-glutamyl-phosphate reductase <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'''
−
|''araR''
+
|''argC''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''araC, yvbS ''
+
|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''' || transcriptional repressor (LacI family))
+
|style="background:#ABCDEF;" align="center"| '''Product''' || N-acetyl-g-glutamyl-phosphate reductase
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || regulation of arabinose utilization
+
|style="background:#ABCDEF;" align="center"|'''Function''' || biosynthesis of arginine
−
(araABDLMNPQ-abfA) and of the araE/araR genes
 
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 43 kDa, 6.341  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 37 kDa, 5.167  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1152 bp, 384 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1038 bp, 346 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[araE]]'', ''[[yvbT]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yitZ]]'', ''[[argJ]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB15402&#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:CAB12960&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:araR_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:argC_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 36: Line 35:
 
=== Basic information ===
 
=== Basic information ===
  
−
* '''Locus tag:''' BSU33970
+
* '''Locus tag:''' BSU11190
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
Line 42: Line 41:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/araR.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/argCJBD-carAB-argF.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11913]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10191]
  
 
=== Additional information===
 
=== Additional information===
Line 53: Line 52:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:'''  
+
* '''Catalyzed reaction/ biological activity:''' N-acetyl-L-glutamate 5-semialdehyde + NADP<sup>+</sup> + phosphate = N-acetyl-5-glutamyl phosphate + NADPH (according to Swiss-Prot)
  
−
* '''Protein family:'''
+
* '''Protein family:''' Type 1 subfamily (according to Swiss-Prot)
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
−
 
−
=== Genes/ operons controlled by AraR ===
 
−
 
−
* '''Activated by AraR:'''
 
−
* ''' Repressed by AraR:''' ''[[araA]]-[[araB]]-[[araD]]-[[araL]]-[[araM]]-[[araN]]-[[araP]]-[[araQ]]-[[abfA]]''
 
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
Line 84: Line 78:
 
* '''Structure:'''
 
* '''Structure:'''
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P96711 P96711]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P23715 P23715]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU33970]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU11190]
  
−
* '''E.C. number:'''
+
* '''E.C. number:''' [http://www.expasy.org/enzyme/1.2.1.38 1.2.1.38]
  
 
=== Additional information===
 
=== Additional information===
Line 94: Line 88:
 
=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:'''
  
 
=Biological materials =
 
=Biological materials =
Line 124: Line 118:
 
=References=
 
=References=
  
−
<pubmed>10417639 9045819, </pubmed>
+
<pubmed>12107147, </pubmed>
−
# Mota LJ, Tavares P, Sá-Nogueira I. (1999) Mode of action of AraR, the key regulator of L-arabinose metabolism in Bacillus subtilis. ''Mol Microbiol.'' '''Aug;33(3):''' 476-89. [http://www.ncbi.nlm.nih.gov/sites/entrez/10417639 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]
−
# Sá-Nogueira I, Mota LJ. (1997) Negative regulation of L-arabinose metabolism in Bacillus subtilis: characterization of the araR (araC) gene. ''J Bacteriol. '' '''Mar;179(5):''' 1598-608. [http://www.ncbi.nlm.nih.gov/sites/entrez/9045819 PubMed]
+
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]

Revision as of 13:08, 8 June 2009

  • Description: N-acetyl-g-glutamyl-phosphate reductase

Gene name argC
Synonyms
Essential no
Product N-acetyl-g-glutamyl-phosphate reductase
Function biosynthesis of arginine
MW, pI 37 kDa, 5.167
Gene length, protein length 1038 bp, 346 aa
Immediate neighbours yitZ, argJ
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
ArgC context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Locus tag: BSU11190

Phenotypes of a mutant

Database entries

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

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity: N-acetyl-L-glutamate 5-semialdehyde + NADP+ + phosphate = N-acetyl-5-glutamyl phosphate + NADPH (according to Swiss-Prot)
  • Protein family: Type 1 subfamily (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

Ulrike Mäder, Georg Homuth, Christian Scharf, Knut Büttner, Rüdiger Bode, Michael Hecker
Transcriptome and proteome analysis of Bacillus subtilis gene expression modulated by amino acid availability.
J Bacteriol: 2002, 184(15);4288-95
[PubMed:12107147] [WorldCat.org] [DOI] (P p)

  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
Retrieved from "https://subtiwiki.uni-goettingen.de/wiki//index.php?title=Sandbox&oldid=88778"