Difference between revisions of "Sandbox"

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* '''Description:''' c-di-GMP specific phosphodiesterase <br/><br/>
+
* '''Description:''' unknown <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'''
|''ykuI''
+
|''ykuH''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
 
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
Line 10: Line 10:
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || c-di-GMP specific phosphodiesterase
+
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
 
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
 
|-
 
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 47 kDa, 4.462  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 21 kDa, 8.896  
 
|-
 
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1221 bp, 407 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 546 bp, 182 aa  
 
|-
 
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ykuH]]'', ''[[fsrA]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[fadG]]'', ''[[ykuI]]''
 
|-
 
|-
 
|colspan="2" style="background:#FAF8CC;" align="center"|'''Hier soll was neues rein'''
 
|colspan="2" style="background:#FAF8CC;" align="center"|'''Hier soll was neues rein'''
 
|-
 
|-
|colspan="2" | '''Genetic context''' <br/> [[Image:ykuI_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:ykuH_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:
 
* '''DBTBS entry:''' no entry
 
* '''DBTBS entry:''' no entry
  
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13293]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13292]
  
 
=== Additional information===
 
=== Additional information===
Line 52: Line 52:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
* '''Catalyzed reaction/ biological activity:''' degradation of cyclic di-GMP  [http://www.ncbi.nlm.nih.gov/sites/entrez/19244251 PubMed]
+
* '''Catalyzed reaction/ biological activity:'''  
  
 
* '''Protein family:'''
 
* '''Protein family:'''
Line 62: Line 62:
 
* '''Kinetic information:'''
 
* '''Kinetic information:'''
  
* '''Domains:''' EAL domain (aa 1 ... 245, for c-di-GMP hydrolysis), PAS-like domain (aa 300 ... 400)  [http://www.ncbi.nlm.nih.gov/sites/entrez/19244251 PubMed]
+
* '''Domains:'''  
  
 
* '''Modification:'''
 
* '''Modification:'''
Line 76: Line 76:
 
=== Database entries ===
 
=== Database entries ===
  
* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=2BAS 2BAS], in complex with c-di-GMP [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=2W27 2W27]  [http://www.ncbi.nlm.nih.gov/sites/entrez/19244251 PubMed]
+
* '''Structure:'''
  
 
* '''Swiss prot entry:'''
 
* '''Swiss prot entry:'''
  
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU14090]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU14080]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
Line 90: Line 90:
 
* '''Operon:'''  
 
* '''Operon:'''  
  
* '''Sigma factor:'''  
+
* '''[[Sigma factor]]:'''  
  
 
* '''Regulation:'''  
 
* '''Regulation:'''  
Line 118: Line 118:
 
=References=
 
=References=
  
# Minasov et al. (2009) Crystal structures of YkuI and its complex with second messenger c-di-GMP suggests catalytic mechanism of phosphodiester bond cleavage by EAL domains ''J. Biol. Chem'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/19244251 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 20:05, 15 April 2009

  • Description: unknown

Gene name ykuH
Synonyms
Essential no
Product unknown
Function unknown
MW, pI 21 kDa, 8.896
Gene length, protein length 546 bp, 182 aa
Immediate neighbours fadG, ykuI
Hier soll was neues rein
Genetic context
YkuH 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