Difference between revisions of "Sandbox"

From SubtiWiki
Jump to: navigation, search
Line 1: Line 1:
−
* '''Description:''' DEAD-box RNA helicase<br/><br/>
+
* '''Description:''' UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine synthetase <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'''
−
|''cshA''
+
|''murF''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ydbR''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ydbQ ''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
+
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || DEAD-box RNA helicase
+
|style="background:#ABCDEF;" align="center"| '''Product''' || UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-<br/>2,6- diaminopimeloyl-D-alanyl-D-alanine synthetase
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || RNA helicase
+
|style="background:#ABCDEF;" align="center"|'''Function''' || peptidoglycan precursor biosynthesis
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 57 kDa, 9.89  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 49 kDa, 5.337  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1533 bp, 511 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1371 bp, 457 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[murF]]'', ''[[ydbS]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ddl]]'', ''[[cshA]]''
 
|-
 
|-
 
|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:ydbR_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:murF_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 30: Line 30:
  
 
<br/><br/>
 
<br/><br/>
 +
 +
 +
 +
 +
  
 
=The gene=
 
=The gene=
Line 38: Line 43:
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
 +
 +
essential [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
  
 
=== Database entries ===
 
=== Database entries ===
Line 43: Line 50:
 
* '''DBTBS entry:''' no entry
 
* '''DBTBS entry:''' no entry
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12085]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12084]
  
 
=== Additional information===
 
=== Additional information===
Line 52: Line 59:
 
=== 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):''' [[CshB]], [[DeaD]], [[YfmL]]
+
* '''Paralogous protein(s):'''
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
Line 72: Line 79:
 
* '''Interactions:'''
 
* '''Interactions:'''
  
−
* '''Localization:''' cytoplasma, colocalizes with the ribosomes [http://www.ncbi.nlm.nih.gov/sites/entrez/16352840 PubMed]
+
* '''Localization:'''
  
 
=== Database entries ===
 
=== Database entries ===
Line 80: Line 87:
 
* '''Swiss prot entry:'''
 
* '''Swiss prot entry:'''
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU04580]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU04570]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
Line 90: Line 97:
 
* '''Operon:'''  
 
* '''Operon:'''  
  
−
* '''Sigma factor:'''  
+
* '''[[Sigma factor]]:'''  
  
 
* '''Regulation:'''  
 
* '''Regulation:'''  
Line 108: Line 115:
 
* '''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=
Line 120: Line 125:
 
=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]
 
−
# Ando, Y. and K. Nakamura (2006) ''Bacillus subtilis'' DEAD protein YdbR possesses ATPase, RNA binding, and RNA unwinding activities.''Biosci. Biotechnol. Biochem.'' '''70:''' 1606-1615. [http://www.ncbi.nlm.nih.gov/sites/entrez/16861794 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 21:14, 15 April 2009

  • Description: UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine synthetase

Gene name murF
Synonyms ydbQ
Essential yes PubMed
Product UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-
2,6- diaminopimeloyl-D-alanyl-D-alanine synthetase
Function peptidoglycan precursor biosynthesis
MW, pI 49 kDa, 5.337
Gene length, protein length 1371 bp, 457 aa
Immediate neighbours ddl, cshA
Hier soll was neues rein
Genetic context
MurF context.gif
This image was kindly provided by SubtiList






The gene

Basic information

  • Coordinates:

Phenotypes of a mutant

essential PubMed

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
Retrieved from "http://subtiwiki.uni-goettingen.de/wiki//index.php?title=Sandbox&oldid=56877"