Difference between revisions of "Sandbox"

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−
* '''Description:''' maybe involved in resistance to bacitracin <br/><br/>
+
* '''Description:''' 3-hydroxyacyl-CoA dehydrogenase (acetoacetyl-CoA) <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'''
−
|''liaI''
+
|''fadN''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yvqI''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yusL''
 
|-
 
|-
 
|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''' || 3-hydroxyacyl-CoA dehydrogenase (acetoacetyl-CoA)
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
+
|style="background:#ABCDEF;" align="center"|'''Function''' || fatty acid degradation
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 13 kDa, 9.303  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 89 kDa, 6.53  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 378 bp, 126 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 2445 bp, 815 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[liaH]]'', ''[[yvqJ]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[fadA]]'', ''[[fadM]]''
 
|-
 
|-
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/yvqI_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/yusL_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/yvqI_protein.txt Protein sequence]'''
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/yusL_protein.txt Protein sequence]'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:yvqI_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:yusL_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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=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yvqIHGFEC.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yusMLKJ.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG14138]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG14024]
  
 
=== Additional information===
 
=== Additional information===
Line 81: Line 81:
 
* '''Swiss prot entry:'''
 
* '''Swiss prot entry:'''
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU33130]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU32840]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
Line 89: Line 89:
 
=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''[[liaI]]-[[liaH]]-[[liaG]]-[[liaF]]-[[liaS]]-[[liaR]]''  
+
* '''Operon:'''  
  
−
* '''Sigma factor:''' [[SigA]]
+
* '''Sigma factor:'''  
  
−
* '''Regulation:''' repressed by glucose (4.3-fold) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed], induced by bacitracin ([[LiaR]])
+
* '''Regulation:''' repressed by glucose (4.5-fold) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]   
  
−
* '''Regulatory mechanism:''' [[LiaR]]: transcription activation
+
* '''Regulatory mechanism:'''  
  
−
* '''Additional information:'''
+
* '''Additional information:'''  
  
 
=Biological materials =
 
=Biological materials =
Line 114: Line 114:
  
 
=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
−
 
−
[[Thorsten Mascher]], Karlsruhe Institute of Technology, Germany [http://microbial-stress.iab.kit.edu/ link]
 
  
 
=Your additional remarks=
 
=Your additional remarks=
Line 122: Line 120:
  
 
# 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]
−
# Jordan, S., A. Junker, J. D. Helmann, and T. Mascher. 2006. Regulation of LiaRS-dependent gene expression in Bacillus subtilis: identification of inhibitor proteins, regulator binding sites, and target genes of a conserved cell envelope stress-sensing two-component system. J. Bacteriol. 188: 5153-5166. [http://www.ncbi.nlm.nih.gov/sites/entrez/16816187 PubMed]
+
# Matsuoka H, Hirooka K, Fujita Y. (2007) Organization and function of the YsiA regulon of Bacillus subtilis involved in fatty acid degradation. ''J Biol Chem. '' '''Feb 23;282(8):''' 5180-94. [http://www.ncbi.nlm.nih.gov/sites/entrez/17189250 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 02:06, 3 April 2009

  • Description: 3-hydroxyacyl-CoA dehydrogenase (acetoacetyl-CoA)

Gene name fadN
Synonyms yusL
Essential no
Product 3-hydroxyacyl-CoA dehydrogenase (acetoacetyl-CoA)
Function fatty acid degradation
MW, pI 89 kDa, 6.53
Gene length, protein length 2445 bp, 815 aa
Immediate neighbours fadA, fadM
Gene sequence (+200bp) Protein sequence
Genetic context
YusL context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Coordinates:

Phenotypes of a mutant

Database entries

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

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: [3]
  • E.C. number:

Additional information

Expression and regulation

  • Operon:
  • Sigma factor:
  • Regulation: repressed by glucose (4.5-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. Matsuoka H, Hirooka K, Fujita Y. (2007) Organization and function of the YsiA regulon of Bacillus subtilis involved in fatty acid degradation. J Biol Chem. Feb 23;282(8): 5180-94. PubMed
  3. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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