Difference between revisions of "Sandbox"

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* '''Description:''' L-arabinose transport (integral membrane protein) <br/><br/>
+
* '''Description:''' acetylornithine transaminase <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'''
|''araP''
+
|''argD''
 
|-
 
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yseD ''
+
|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''' || L-arabinose transport (integral membrane protein))
+
|style="background:#ABCDEF;" align="center"| '''Product''' || acetylornithine transaminase
 
|-
 
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || uptake of arabinose
+
|style="background:#ABCDEF;" align="center"|'''Function''' || biosynthesis of arginine
 
|-
 
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 34 kDa, 9.69  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 40 kDa, 5.929  
 
|-
 
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 939 bp, 313 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1155 bp, 385 aa  
 
|-
 
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[araQ]]'', ''[[araN]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[argB]]'', ''[[carA]]''
 
|-
 
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB14834&#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:CAB12963&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
|colspan="2" | '''Genetic context''' <br/> [[Image:araP_context.gif]]
+
|-
 +
|-
 +
|colspan="2" | '''Genetic context''' <br/> [[Image:argD_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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__TOC__
 
__TOC__
  
<br/><br/>
+
<br/><br/><br/><br/>
  
 
=The gene=
 
=The gene=
Line 35: Line 37:
 
=== Basic information ===
 
=== Basic information ===
  
* '''Locus tag:''' BSU28740
+
* '''Locus tag:''' BSU11220
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
Line 41: Line 43:
 
=== Database entries ===
 
=== Database entries ===
  
* '''DBTBS entry:''' no entry
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/argCJBD-carAB-argF.html]
  
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11911]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10194]
  
 
=== Additional information===
 
=== Additional information===
Line 52: Line 54:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
* '''Catalyzed reaction/ biological activity:'''  
+
* '''Catalyzed reaction/ biological activity:''' N(2)-acetyl-L-ornithine + 2-oxoglutarate = N-acetyl-L-glutamate 5-semialdehyde + L-glutamate (according to Swiss-Prot)
  
* '''Protein family:''' MalFG subfamily (according to Swiss-Prot)
+
* '''Protein family:''' ArgD subfamily (according to Swiss-Prot)
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
Line 72: Line 74:
 
* '''Interactions:'''
 
* '''Interactions:'''
  
* '''Localization:''' cell membrane (according to Swiss-Prot)
+
* '''Localization:''' cytoplasm (according to Swiss-Prot)
  
 
=== Database entries ===
 
=== Database entries ===
Line 78: Line 80:
 
* '''Structure:'''
 
* '''Structure:'''
  
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P94529 P94529]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P36839 P36839]
  
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU28740]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU11220]
  
* '''E.C. number:'''
+
* '''E.C. number:''' [http://www.expasy.org/enzyme/2.6.1.11 2.6.1.11]
  
 
=== Additional information===
 
=== Additional information===
Line 88: Line 90:
 
=Expression and regulation=
 
=Expression and regulation=
  
* '''Operon:''' ''[[araA]]-[[araB]]-[[araD]]-[[araL]]-[[araM]]-[[araN]]-[[araP]]-[[araQ]]-[[abfA]]''
+
* '''Operon:''' ''[[argC]]-[[argJ]]-[[argB]]-[[argD]]-[[carA]]-[[carB]]-[[argF]]''
  
 
* '''[[Sigma factor]]:''' [[SigA]]
 
* '''[[Sigma factor]]:''' [[SigA]]
  
* '''Regulation:''' repressed by glucose ([[CcpA]])
+
* '''Regulation:''' repressed by casamino acids [http://www.ncbi.nlm.nih.gov/pubmed/12107147 PubMed], repressed by arginine ([[AhrC]])
  
* '''Regulatory mechanism:''' [[CcpA]]: transcription repression  
+
* '''Regulatory mechanism:''' [[AhrC]]: transcription repression
  
* '''Additional information:''' the mRNA is very stable (half-life > 15 min) [http://www.ncbi.nlm.nih.gov/sites/entrez/12884008 PubMed]
+
* '''Additional information:'''
  
 
=Biological materials =
 
=Biological materials =
Line 118: Line 120:
 
=References=
 
=References=
  
<pubmed>12949161 9084180, </pubmed>
+
<pubmed>12107147, </pubmed>
# Inácio JM, Costa C, de Sá-Nogueira I. (2003) Distinct molecular mechanisms involved in carbon catabolite repression of the arabinose regulon in Bacillus subtilis. ''Microbiology. '' '''Sep;149(Pt 9):''' 2345-55. [http://www.ncbi.nlm.nih.gov/sites/entrez/12949161 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]
# Sa-Nogueira I.M.G., Nogueira T.V., Soares S., de Lencastre H. (1997) The Bacillus subtilis L-arabinose (ara) operon: nucleotide sequence, genetic organization and expression. ''Microbiology.'' '''Mar;143(Pt 3):''' 957-69. [http://www.ncbi.nlm.nih.gov/sites/entrez/9084180 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 13:56, 8 June 2009

  • Description: acetylornithine transaminase

Gene name argD
Synonyms
Essential no
Product acetylornithine transaminase
Function biosynthesis of arginine
MW, pI 40 kDa, 5.929
Gene length, protein length 1155 bp, 385 aa
Immediate neighbours argB, carA
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
ArgD context.gif
This image was kindly provided by SubtiList





The gene

Basic information

  • Locus tag: BSU11220

Phenotypes of a mutant

Database entries

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

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity: N(2)-acetyl-L-ornithine + 2-oxoglutarate = N-acetyl-L-glutamate 5-semialdehyde + L-glutamate (according to Swiss-Prot)
  • Protein family: ArgD 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