Difference between revisions of "Sandbox"

From SubtiWiki
Jump to: navigation, search
Line 1: Line 1:
* '''Description:''' inositol 2-dehydrogenase <br/><br/>
+
* '''Description:''' similar to ABC transporter (ATP-binding protein) <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''
+
|''yxdL''
 
|-
 
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''idh, iol ''
+
|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''' || inositol 2-dehydrogenase
+
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
 
|-
 
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || myo-inositol catabolism
+
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
 
|-
 
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 38 kDa, 4.865  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 28 kDa, 7.365  
 
|-
 
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1032 bp, 344 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 771 bp, 257 aa  
 
|-
 
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[iolH]]'', ''[[iolF]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yxdM]]'', ''[[yxdK]]''
 
|-
 
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB16006&#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:CAB16000&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
 
|-
 
|-
 
|-
 
|-
|colspan="2" | '''Genetic context''' <br/> [[Image:idh_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:yxdL_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 43: Line 43:
 
=== Database entries ===
 
=== Database entries ===
  
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/mmsA-iolBCDEF-idh-iolHI-fbaB.html]
+
* '''DBTBS entry:''' no entry
  
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10669]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11128]
  
 
=== Additional information===
 
=== Additional information===
Line 82: Line 82:
 
* '''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+BSU39640]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
Line 90: Line 90:
 
=Expression and regulation=
 
=Expression and regulation=
  
* '''Operon:''' ''[[iolA]]-[[iolB]]-[[iolC]]-[[iolD]]-[[iolE]]-[[iolF]]-[[iolG]]-[[iolH]]-[[iolJ]]''
+
* '''Operon:'''  
  
* '''Sigma factor:''' [[SigA]]
+
* '''[[Sigma factor]]:'''  
  
* '''Regulation:''' repressed by glucose ([[CcpA]])
+
* '''Regulation:'''  
  
* '''Regulatory mechanism:''' [[CcpA]]: transcription repression,  [[CcpA]]: transcription repression
+
* '''Regulatory mechanism:'''  
  
* '''Additional information:'''
+
* '''Additional information:'''  
  
 
=Biological materials =
 
=Biological materials =
Line 120: Line 120:
 
=References=
 
=References=
  
 
+
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID 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 23:50, 16 April 2009

  • Description: similar to ABC transporter (ATP-binding protein)

Gene name yxdL
Synonyms
Essential no
Product unknown
Function unknown
MW, pI 28 kDa, 7.365
Gene length, protein length 771 bp, 257 aa
Immediate neighbours yxdM, yxdK
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
YxdL context.gif
This image was kindly provided by SubtiList





The gene

Basic information

  • Coordinates:

Phenotypes of a mutant

Database entries

  • DBTBS entry: no entry
  • SubtiList entry: [1]

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: [2]
  • 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