Difference between revisions of "Sandbox"

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−
* '''Description:''' DEAD-box RNA helicase<br/><br/>
+
* '''Description:''' type IV apurinic/apyrimidinic endonuclease <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'''
−
|''cshB ''
+
|''nfo ''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yqfR''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yqfS''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || DEAD-box RNA helicase
+
|style="background:#ABCDEF;" align="center"| '''Product''' || type IV apurinic/apyrimidinic endonuclease
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || RNA helicase
+
|style="background:#ABCDEF;" align="center"|'''Function''' || repair of oxidative DNA damage in spores
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 49 kDa, 9.89  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 32 kDa, 5.371  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1314 bp, 438 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 891 bp, 297 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[nfo]]'', ''[[yqfQ]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yqfT]]'', ''[[cshB]]''
 
|-
 
|-
 
|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:yqfR_context.gif]]
+
|-
 +
|-
 +
|colspan="2" | '''Genetic context''' <br/> [[Image:yqfS_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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__TOC__
 
__TOC__
  
−
<br/><br/>
+
<br/><br/><br/><br/>
  
 
=The gene=
 
=The gene=
Line 41: Line 43:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' no entry
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yqfSU.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11664]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11665]
  
 
=== Additional information===
 
=== Additional information===
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=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:''' RNA helicase
+
* '''Catalyzed reaction/ biological activity:'''  
  
−
* '''Protein family:''' DEAD-box RNA helicase
+
* '''Protein family:'''
  
−
* '''Paralogous protein(s):''' [[CshA]], [[DeaD]], [[YfmL]]
+
* '''Paralogous protein(s):'''
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
Line 70: Line 72:
 
* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
  
−
* '''Interactions:''' [[CshB]]-[[CspB]] [http://www.ncbi.nlm.nih.gov/sites/entrez/16352840 PubMed]
+
* '''Interactions:'''
  
−
* '''Localization:''' cytoplasma, colocalizes with the ribosomes [http://www.ncbi.nlm.nih.gov/sites/entrez/16352840 PubMed]
+
* '''Localization:'''
  
 
=== Database entries ===
 
=== Database entries ===
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* '''Swiss prot entry:'''
 
* '''Swiss prot entry:'''
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU25140]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU25130]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
Line 90: Line 92:
 
* '''Operon:'''  
 
* '''Operon:'''  
  
−
* '''Sigma factor:'''  
+
* '''[[Sigma factor]]:'''  
  
 
* '''Regulation:'''  
 
* '''Regulation:'''  
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* '''GFP fusion:'''
 
* '''GFP fusion:'''
  
−
* '''two-hybrid system:''' B. pertussis adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Stülke]] lab
+
* '''two-hybrid system:'''  
  
 
* '''Antibody:'''
 
* '''Antibody:'''
  
 
=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
−
 
−
[[Mohamed Marahiel]], Marburg University, Germany [http://www.uni-marburg.de/fb15/fachgebiete/bio/marahiel?language_sync=1 homepage]
 
  
 
=Your additional remarks=
 
=Your additional remarks=
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=References=
 
=References=
  
−
# Hunger, K., Beckering, C. L., Wiegeshoff, F., Graumann, P. L. & Marahiel, M. A. (2006). Cold-induced putative DEAD box RNA helicases CshA and CshB are essential for cold adaptation and interact with cold shock protein B in ''Bacillus subtilis''. J Bacteriol. 188:240-248. [http://www.ncbi.nlm.nih.gov/sites/entrez/16352840 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 18:45, 15 April 2009

  • Description: type IV apurinic/apyrimidinic endonuclease

Gene name nfo
Synonyms yqfS
Essential no
Product type IV apurinic/apyrimidinic endonuclease
Function repair of oxidative DNA damage in spores
MW, pI 32 kDa, 5.371
Gene length, protein length 891 bp, 297 aa
Immediate neighbours yqfT, cshB
Hier soll was neues rein
Genetic context
YqfS 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

  • 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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