Difference between revisions of "Sandbox"

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−
* '''Description:''' beta-1,4-mannosidase <br/><br/>
+
* '''Description:''' write here <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'''
−
|''gmuG''
+
|''xynC ''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ydhT''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ynfF''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || beta-1,4-mannosidase
+
|style="background:#ABCDEF;" align="center"| '''Product''' ||  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || glucomannan utilization
+
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 40 kDa, 5.628  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 47 kDa, 9.078  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1086 bp, 362 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1266 bp, 422 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[gmuF]]'', ''[[ydhU]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ynfE]]'', ''[[xynD]]''
 
|-
 
|-
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/ydhT_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/ynfF_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/ydhT_protein.txt Protein sequence]'''
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/ynfF_protein.txt Protein sequence]'''
 
|-
 
|-
−
|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:ynfF_context.gif]]
−
|-
 
−
|colspan="2" | '''Genetic context''' <br/> [[Image:ydhT_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 44: Line 42:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/gmuBACDREFG.html]
+
* '''DBTBS entry:''' no entry
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12197]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11830]
  
 
=== Additional information===
 
=== Additional information===
Line 83: Line 81:
 
* '''Swiss prot entry:'''
 
* '''Swiss prot entry:'''
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU05880]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU18150]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
Line 91: Line 89:
 
=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''[[gmuB]]-[[gmuA]]-[[gmuC]]-[[gmuD]]-[[gmuR]]-[[gmuE]]-[[gmuF]]-[[gmuG]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/18177310 PubMed]
+
* '''Operon:'''  
  
−
* '''Sigma factor:''' [[SigA]]
+
* '''Sigma factor:'''  
  
 
* '''Regulation:'''  
 
* '''Regulation:'''  
Line 99: Line 97:
 
* '''Regulatory mechanism:'''  
 
* '''Regulatory mechanism:'''  
  
−
* '''Additional information:'''
+
* '''Additional information:'''  
  
 
=Biological materials =
 
=Biological materials =
Line 122: Line 120:
  
 
# Voigt et al. (2009) Cell physiology and protein secretion of Bacillus licheniformis compared to ''Bacillus subtilis''. ''J Mol Microbiol Biotechnol.'' '''16:''' 53-68 [http://www.ncbi.nlm.nih.gov/pubmed/18957862 PubMed]
 
# Voigt et al. (2009) Cell physiology and protein secretion of Bacillus licheniformis compared to ''Bacillus subtilis''. ''J Mol Microbiol Biotechnol.'' '''16:''' 53-68 [http://www.ncbi.nlm.nih.gov/pubmed/18957862 PubMed]
−
# Sadaie Y, Nakadate H, Fukui R, Yee LM, Asai K. (2008) Glucomannan utilization operon of Bacillus subtilis. ''FEMS Microbiol Lett.'' '''Feb;279(1):''' 103-9. [http://www.ncbi.nlm.nih.gov/sites/entrez/18177310 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 16:25, 6 April 2009

  • Description: write here

Gene name xynC
Synonyms ynfF
Essential no
Product
Function unknown
MW, pI 47 kDa, 9.078
Gene length, protein length 1266 bp, 422 aa
Immediate neighbours ynfE, xynD
Gene sequence (+200bp) Protein sequence
Genetic context
YnfF 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: extracellular (signal peptide) PubMed

Database entries

  • Structure:
  • Swiss prot entry:
  • KEGG entry: [2]
  • E.C. number:

Additional information

Expression and regulation

  • Operon:
  • Sigma factor:
  • 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. Voigt et al. (2009) Cell physiology and protein secretion of Bacillus licheniformis compared to Bacillus subtilis. J Mol Microbiol Biotechnol. 16: 53-68 PubMed
  2. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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