Difference between revisions of "Sandbox"

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−
* '''Description:''' similar to iron-sulphur-binding reductase <br/><br/>
+
* '''Description:''' oxidoreductase <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'''
−
|''fadF''
+
|''yydG''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ywjF ''
+
|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''' || oxidoreductase
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || fatty acid degradation
+
|style="background:#ABCDEF;" align="center"|'''Function''' || control of LiaRS activity
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 79 kDa, 6.526  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 37 kDa, 5.865  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 2115 bp, 705 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 957 bp, 319 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[acdA]]'', ''[[ywjE]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yydH]]'', ''[[yydF]]''
 
|-
 
|-
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/ywjF_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/yydG_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/ywjF_protein.txt Protein sequence]'''
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/yydG_protein.txt Protein sequence]'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:ywjF_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:yydG_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/ywjF-acdA-rpoE.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yydFGHIJ.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11311]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11480]
  
 
=== 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+BSU37180]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU40170]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
Line 89: Line 89:
 
=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:'''  
+
* '''Operon:''' ''[[yydF]]-[[yydG]]-[[yydH]]-[[yydI]]-[[yydJ]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/17921301 PubMed]
  
−
* '''Sigma factor:'''  
+
* '''Sigma factor:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/17921301 PubMed]
  
−
* '''Regulation:''' repressed by glucose (5-fold) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]   
+
* '''Regulation:''' repressed by glucose (5-fold) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed], activated after transition to stationary phase([[AbrB]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/17921301 PubMed]
  
−
* '''Regulatory mechanism:'''  
+
* '''Regulatory mechanism:''' [[AbrB]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/17921301 PubMed]
  
 
* '''Additional information:'''  
 
* '''Additional information:'''  
Line 120: 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]
−
# 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]
+
# Butcher BG, Lin YP, Helmann JD (2007) The ''yydFGHIJ'' operon of ''Bacillus subtilis'' encodes a peptide that induces the LiaRS two-component system''J. Bacteriol'' '''189:''' 8616-8625. [http://www.ncbi.nlm.nih.gov/sites/entrez/17921301 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: oxidoreductase

Gene name yydG
Synonyms
Essential no
Product oxidoreductase
Function control of LiaRS activity
MW, pI 37 kDa, 5.865
Gene length, protein length 957 bp, 319 aa
Immediate neighbours yydH, yydF
Gene sequence (+200bp) Protein sequence
Genetic context
YydG 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

  • Regulation: repressed by glucose (5-fold) PubMed, activated after transition to stationary phase(AbrB) PubMed
  • Regulatory mechanism: AbrB: transcription repression PubMed
  • 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. Butcher BG, Lin YP, Helmann JD (2007) The yydFGHIJ operon of Bacillus subtilis encodes a peptide that induces the LiaRS two-component systemJ. Bacteriol 189: 8616-8625. PubMed
  3. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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