Difference between revisions of "Sandbox"

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−
* '''Description:''' similar to Ser/Thr kinase <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'''
−
|''yxaL''
+
|''yxbB''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yxaK ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yxaP ''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
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|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
 
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 43 kDa, 6.379  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 28 kDa, 4.569  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1230 bp, 410 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 732 bp, 244 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yxaM]]'', ''[[yxaJ]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yxbC]]'', ''[[yxbA]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB16030&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
+
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB16025&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|-
+
|colspan="2" | '''Genetic context''' <br/> [[Image:yxbB_context.gif]]
−
|-
 
−
|colspan="2" | '''Genetic context''' <br/> [[Image:yxaL_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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=== Basic information ===
 
=== Basic information ===
  
−
* '''Locus tag:''' BSU39940
+
* '''Locus tag:''' BSU39890
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
Line 43: Line 41:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yxaJL.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yxbBA-yxnB-asnH-yxaM.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11114]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11352]
  
 
=== Additional information===
 
=== Additional information===
Line 56: Line 54:
 
* '''Catalyzed reaction/ biological activity:'''  
 
* '''Catalyzed reaction/ biological activity:'''  
  
−
* '''Protein family:'''
+
* '''Protein family:''' methyltransferase superfamily (according to Swiss-Prot)
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
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* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
  
−
* '''Interactions:''' [[YxaL]]-[[PcrA]]
+
* '''Interactions:'''
  
−
* '''Localization:''' secreted (according to Swiss-Prot),  extracellular (signal peptide) [http://www.ncbi.nlm.nih.gov/pubmed/18957862 PubMed]
+
* '''Localization:'''
  
 
=== Database entries ===
 
=== Database entries ===
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* '''Structure:'''
 
* '''Structure:'''
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P42111 P42111]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P46326 P46326]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU39940]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU39890]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
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=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''[[yxaJ]]-[[yxaL]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/10746760 PubMed]
+
* '''Operon:''' ''[[yxbB]]-[[yxbA]]-[[yxnB]]-[[asnH]]-[[yxaM]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/10746760 PubMed]
  
 
* '''[[Sigma factor]]:'''  
 
* '''[[Sigma factor]]:'''  
  
−
* '''Regulation:'''  
+
* '''Regulation:''' repressed by glucose (8-fold) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed], repressed by [[CodY]] [http://www.ncbi.nlm.nih.gov/sites/entrez/12618455 PubMed]
  
−
* '''Regulatory mechanism:'''  
+
* '''Regulatory mechanism:''' [[CodY]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/12618455 PubMed1]  [http://www.ncbi.nlm.nih.gov/sites/entrez/18083814 PubMed2]
  
 
* '''Additional information:'''
 
* '''Additional information:'''
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* '''Mutant:'''
 
* '''Mutant:'''
  
−
* '''Expression vector:''' pGP392 (N-terminal Strep-tag, purification from ''B. subtilis'', for [[SPINE]], in [[pGP380]]), available in [[Stülke]] lab
+
* '''Expression vector:'''
 
          
 
          
 
* '''lacZ fusion:'''
 
* '''lacZ fusion:'''
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=References=
 
=References=
  
−
<pubmed>18957862, </pubmed>
+
<pubmed>12850135, </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]
+
# Blencke et al. (2003) Transcriptional profiling of gene expression in response to glucose in ''Bacillus subtilis'': regulation of the central metabolic pathways. ''Metab Eng.'' '''5:''' 133-149 [http://www.ncbi.nlm.nih.gov/pubmed/12850135 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 13:54, 8 June 2009

  • Description: unknown

Gene name yxbB
Synonyms yxaP
Essential no
Product unknown
Function unknown
MW, pI 28 kDa, 4.569
Gene length, protein length 732 bp, 244 aa
Immediate neighbours yxbC, yxbA
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
YxbB context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Locus tag: BSU39890

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: methyltransferase superfamily (according to Swiss-Prot)
  • Paralogous protein(s):

Extended information on the protein

  • Kinetic information:
  • Domains:
  • Modification:
  • Cofactor(s):
  • Effectors of protein activity:
  • Interactions:
  • Localization:

Database entries

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

Additional information

Expression and regulation

  • 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

Hans-Matti Blencke, Georg Homuth, Holger Ludwig, Ulrike Mäder, Michael Hecker, Jörg Stülke
Transcriptional profiling of gene expression in response to glucose in Bacillus subtilis: regulation of the central metabolic pathways.
Metab Eng: 2003, 5(2);133-49
[PubMed:12850135] [WorldCat.org] [DOI] (P p)

  1. Blencke et al. (2003) Transcriptional profiling of gene expression in response to glucose in Bacillus subtilis: regulation of the central metabolic pathways. Metab Eng. 5: 133-149 PubMed
  2. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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