Difference between revisions of "Sandbox"

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−
* '''Description:''' glucose 1-dehydrogenase (NAD) <br/><br/>
+
* '''Description:''' malic enzyme <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'''
−
|''gdh''
+
|''ycsA''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
 
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
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|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || glucose 1-dehydrogenase (NAD)
+
|style="background:#ABCDEF;" align="center"| '''Product''' || D-malate dehydrogenase (NAD)  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || germination
+
|style="background:#ABCDEF;" align="center"|'''Function''' || malic enzyme, links TCA cycle to gluconeogenesis
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 27 kDa, 5.082  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 38 kDa, 5.108  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 783 bp, 261 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1062 bp, 354 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[glcU]]'', ''[[ycnI]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[mtlD]]'', ''[[sipU]]''
 
|-
 
|-
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/gdh_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/ycsA_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/gdh_protein.txt Protein sequence]'''
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/ycsA_protein.txt Protein sequence]'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:gdh_context.gif]]
+
|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:ycsA_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/glcU-gdh.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ycsA.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10545]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11222]
  
 
=== Additional information===
 
=== Additional information===
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* '''Catalyzed reaction/ biological activity:'''  
 
* '''Catalyzed reaction/ biological activity:'''  
  
−
* '''Protein family:''' short-chain dehydrogenases/reductases (SDR) family
+
* '''Protein family:''' isocitrate and isopropylmalate dehydrogenases family
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
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* '''Swiss prot entry:'''
 
* '''Swiss prot entry:'''
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU03930]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU04000]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''

Revision as of 03:21, 12 April 2009

  • Description: malic enzyme

Gene name ycsA
Synonyms
Essential no
Product D-malate dehydrogenase (NAD)
Function malic enzyme, links TCA cycle to gluconeogenesis
MW, pI 38 kDa, 5.108
Gene length, protein length 1062 bp, 354 aa
Immediate neighbours mtlD, sipU
Gene sequence (+200bp) Protein sequence
Caution: The sequence for this gene in SubtiList contains errors
Genetic context
YcsA 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: isocitrate and isopropylmalate dehydrogenases 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:
  • Regulation:
  • 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. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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