Difference between revisions of "Sandbox"

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* '''Description:''' inositol 2-dehydrogenase <br/><br/>
+
* '''Description:''' 2-deoxy-5-keto-gluconic acid-6-phosphate aldolase, formation of dihydroxyacetone phosphate and malonic semialdehyde (6th reaction) <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'''
−
|''iolG''
+
|''iolJ''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''idh, iol ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''fbaB, yxdI ''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || inositol 2-dehydrogenase
+
|style="background:#ABCDEF;" align="center"| '''Product''' || 2-deoxy-5-keto-gluconic acid-6-phosphate aldolase, <br/>formation of dihydroxyacetone phosphate and <br/>malonic semialdehyde (6th reaction)
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"|'''Function''' || myo-inositol catabolism
 
|style="background:#ABCDEF;" align="center"|'''Function''' || myo-inositol catabolism
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 38 kDa, 4.865  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 31 kDa, 4.854  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1032 bp, 344 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 870 bp, 290 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[iolH]]'', ''[[iolF]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yxdJ]]'', ''[[iolI]]''
 
|-
 
|-
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/idh_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/fbaB_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/idh_protein.txt Protein sequence]'''
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/fbaB_protein.txt Protein sequence]'''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;color:#FF0000" align="center" | '''Caution: The sequence for this gene in SubtiList contains errors
+
|colspan="2" | '''Genetic context''' <br/> [[Image:fbaB_context.gif]]
−
|-
 
−
|colspan="2" | '''Genetic context''' <br/> [[Image:idh_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 46: Line 44:
 
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/mmsA-iolBCDEF-idh-iolHI-fbaB.html]
 
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/mmsA-iolBCDEF-idh-iolHI-fbaB.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10669]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11125]
  
 
=== Additional information===
 
=== Additional information===
Line 59: Line 57:
 
* '''Protein family:'''
 
* '''Protein family:'''
  
−
* '''Paralogous protein(s):'''
+
* '''Paralogous protein(s):''' [[FbaA]]
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
Line 71: Line 69:
 
* '''Cofactor(s):'''
 
* '''Cofactor(s):'''
  
−
* '''Effectors of protein activity:'''
+
* '''Effectors of protein activity:''' inhibited by alpha-keto acids [http://www.ncbi.nlm.nih.gov/pubmed/24624 PubMed]
  
 
* '''Interactions:'''
 
* '''Interactions:'''
Line 83: Line 81:
 
* '''Swiss prot entry:'''
 
* '''Swiss prot entry:'''
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU39700]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU39670]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
Line 95: Line 93:
 
* '''Sigma factor:''' [[SigA]]
 
* '''Sigma factor:''' [[SigA]]
  
−
* '''Regulation:''' repressed by glucose ([[CcpA]])  
+
* '''Regulation:''' repressed by glucose ([[CcpA]])
  
 
* '''Regulatory mechanism:''' [[CcpA]]: transcription repression  
 
* '''Regulatory mechanism:''' [[CcpA]]: transcription repression  
Line 123: Line 121:
 
# 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  
 
# 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  
 
# Yoshida K, Yamaguchi M, Morinaga T, Kinehara M, Ikeuchi M, Ashida H, Fujita Y. (2008) myo-Inositol catabolism in Bacillus subtilis. ''J Biol Chem. '' ''' Apr 18;283(16):''' 10415-24. [http://www.ncbi.nlm.nih.gov/sites/entrez/18310071 PubMed]
 
# Yoshida K, Yamaguchi M, Morinaga T, Kinehara M, Ikeuchi M, Ashida H, Fujita Y. (2008) myo-Inositol catabolism in Bacillus subtilis. ''J Biol Chem. '' ''' Apr 18;283(16):''' 10415-24. [http://www.ncbi.nlm.nih.gov/sites/entrez/18310071 PubMed]
−
# Ramaley R, Fujita Y, Freese E. (1979) Purification and properties of Bacillus subtilis inositol dehydrogenase. ''J Biol Chem.'' '''Aug 25;254(16):''' 7684-90. [http://www.ncbi.nlm.nih.gov/sites/entrez/112095 PubMed]
 

Revision as of 00:44, 3 April 2009

  • Description: 2-deoxy-5-keto-gluconic acid-6-phosphate aldolase, formation of dihydroxyacetone phosphate and malonic semialdehyde (6th reaction)

Gene name iolJ
Synonyms fbaB, yxdI
Essential no
Product 2-deoxy-5-keto-gluconic acid-6-phosphate aldolase,
formation of dihydroxyacetone phosphate and
malonic semialdehyde (6th reaction)
Function myo-inositol catabolism
MW, pI 31 kDa, 4.854
Gene length, protein length 870 bp, 290 aa
Immediate neighbours yxdJ, iolI
Gene sequence (+200bp) Protein sequence
Genetic context
FbaB 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): FbaA

Extended information on the protein

  • Kinetic information:
  • Domains:
  • Modification:
  • Cofactor(s):
  • Effectors of protein activity: inhibited by alpha-keto acids PubMed
  • Interactions:
  • Localization:

Database entries

  • Structure:
  • Swiss prot entry:
  • KEGG entry: [3]
  • E.C. number:

Additional information

Expression and regulation

  • Regulation: repressed by glucose (CcpA)
  • Regulatory mechanism: CcpA: 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. 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
  2. Yoshida K, Yamaguchi M, Morinaga T, Kinehara M, Ikeuchi M, Ashida H, Fujita Y. (2008) myo-Inositol catabolism in Bacillus subtilis. J Biol Chem. Apr 18;283(16): 10415-24. PubMed
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