Difference between revisions of "Sandbox"

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−
* '''Description:''' arabinoxylan arabinofuranohydrolase <br/><br/>
+
* '''Description:''' beta-1,4-mannosidase <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'''
−
|''xynD''
+
|''gmuG''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ydhT''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || arabinoxylan arabinofuranohydrolase
+
|style="background:#ABCDEF;" align="center"| '''Product''' || beta-1,4-mannosidase
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || arabinoxylan degradation
+
|style="background:#ABCDEF;" align="center"|'''Function''' || glucomannan utilization
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 54 kDa, 8.031  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 40 kDa, 5.628  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1539 bp, 513 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1086 bp, 362 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[xynC]]'', ''[[yngA]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[gmuF]]'', ''[[ydhU]]''
 
|-
 
|-
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/xynD_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
+
|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/xynD_protein.txt Protein sequence]'''
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/ydhT_protein.txt Protein sequence]'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:xynD_context.gif]]
+
|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: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>
 
|-
 
|-
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=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' no entry
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/gmuBACDREFG.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11807]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12197]
  
 
=== Additional information===
 
=== Additional information===
Line 77: Line 79:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=3C7O 3C7O]
+
* '''Structure:'''
  
 
* '''Swiss prot entry:'''
 
* '''Swiss prot entry:'''
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU18160]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU05880]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
Line 89: Line 91:
 
=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:'''  
+
* '''Operon:''' ''[[gmuB]]-[[gmuA]]-[[gmuC]]-[[gmuD]]-[[gmuR]]-[[gmuE]]-[[gmuF]]-[[gmuG]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/18177310 PubMed]
  
−
* '''Sigma factor:'''  
+
* '''Sigma factor:''' [[SigA]]
  
 
* '''Regulation:'''  
 
* '''Regulation:'''  
Line 97: Line 99:
 
* '''Regulatory mechanism:'''  
 
* '''Regulatory mechanism:'''  
  
−
* '''Additional information:'''  
+
* '''Additional information:'''
  
 
=Biological materials =
 
=Biological materials =
Line 120: Line 122:
  
 
# 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: beta-1,4-mannosidase

Gene name gmuG
Synonyms ydhT
Essential no
Product beta-1,4-mannosidase
Function glucomannan utilization
MW, pI 40 kDa, 5.628
Gene length, protein length 1086 bp, 362 aa
Immediate neighbours gmuF, ydhU
Gene sequence (+200bp) Protein sequence
Caution: The sequence for this gene in SubtiList contains errors
Genetic context
YdhT 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: extracellular (signal peptide) PubMed

Database entries

  • Structure:
  • Swiss prot entry:
  • KEGG entry: [3]
  • E.C. number:

Additional information

Expression and regulation

  • 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. 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. PubMed
  3. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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