Difference between revisions of "Sandbox"

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* '''Description:''' Enzyme I, general (non sugar-specific) component of the PTS. Enzyme I transfers the phosphoryl group from phosphoenolpyruvate (PEP) to the phosphoryl carrier protein ([[PtsH |HPr]])  <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'''
−
|''ptsI''
+
|''ykwB''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
 
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
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|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || phosphotransferase system (PTS) enzyme I
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|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || PTS-dependent sugar transport
+
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 62,9 kDa, 4.59
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 19 kDa, 5.946 
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1710 bp, 570 amino acids
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 519 bp, 173 aa
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ptsH]]'', ''[[splA]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[splB]]'', ''[[mcpC]]''
 
|-
 
|-
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/ptsI_nucleotide.txt    Gene sequence      (+200bp) ]'''  
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/ykwB_nucleotide.txt    Gene sequence      (+200bp)   ]'''  
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/ptsI_protein.txt Protein sequence]'''
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/ykwB_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:ykwB_context.gif]]
−
|-
 
−
|colspan="2" | '''Genetic context''' <br/> [[Image:ptsI_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=
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=== Basic information ===
 
=== Basic information ===
  
−
* '''Coordinates:''' 1458959 - 1460668
+
* '''Coordinates:'''
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
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=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ptsGHI.html]
+
* '''DBTBS entry:''' no entry
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10201]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12252]
  
 
=== Additional information===
 
=== Additional information===
 +
  
 
=The protein=
 
=The protein=
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=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:''' PEP-dependent autophosphorylation on His-189, transfer of the phosphoryl group to [[PtsH |HPr]] (His-15)
+
* '''Catalyzed reaction/ biological activity:'''  
  
−
* '''Protein family:''' PEP-utilizing enzyme family PEP-utilizing enzyme family
+
* '''Protein family:''' N-acetyltransferase domain
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
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* '''Domains:'''  
 
* '''Domains:'''  
−
**HPr binding site (N-Terminal Domain)
 
−
**pyruvate binding site (C-Terminal Domain)
 
−
**pyrophosphate/phosphate carrier histidine (central Domain)
 
  
−
* '''Modification:''' transient autophosphorylation on His-189, in vivo also phosphorylated on Ser-34 or Ser-36 [http://www.ncbi.nlm.nih.gov/pubmed/17218307 PubMed]
+
* '''Modification:'''
  
−
* '''Cofactor(s):''' Magnesium
+
* '''Cofactor(s):'''
  
 
* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
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* '''Interactions:'''
 
* '''Interactions:'''
  
−
* '''Localization:''' Cytoplasm
+
* '''Localization:'''
  
 
=== Database entries ===
 
=== Database entries ===
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* '''Structure:'''
 
* '''Structure:'''
  
−
* '''Swiss prot entry:''' [http://www.expasy.ch/cgi-bin/sprot-search-ac?P08838]
+
* '''Swiss prot entry:'''
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU13910]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU13940]
  
−
* '''E.C. number:''' [http://www.expasy.org/enzyme/2.7.3.9 2.7.3.9]
+
* '''E.C. number:'''
  
 
=== Additional information===
 
=== Additional information===
−
 
  
 
=Expression and regulation=
 
=Expression and regulation=
  
 
* '''Operon:'''  
 
* '''Operon:'''  
−
**''[[ptsG]]-[[ptsH]]-[[ptsI]]''
 
−
**''[[ptsH]]-[[ptsI]]''
 
  
−
* '''[[Sigma factor]]:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+11902727 PubMed]
+
* '''[[Sigma factor]]:'''  
−
* '''Regulation:''' expression activated by glucose (4.3 fold) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed],  induction by glucose (''[[ptsG]]''), constitutive (''[[ptsH]]'')
 
  
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* '''Regulatory mechanism:''' ''[[ptsG]]'': transcriptional antitermination via the [[GlcT]]-dependent RNA-switch
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* '''Regulation:'''  
  
−
* '''Additional information:'''
+
* '''Regulatory mechanism:'''
 +
 
 +
* '''Additional information:'''  
  
 
=Biological materials =
 
=Biological materials =
  
−
* '''Mutant:''' GP864 (ermC), available in [[Stülke]] lab
+
* '''Mutant:'''
  
−
* '''Expression vector:''' pAG3 (His-tag), available in [[Galinier]] lab
+
* '''Expression vector:'''
−
+
       
 
* '''lacZ fusion:'''
 
* '''lacZ fusion:'''
  
 
* '''GFP fusion:'''
 
* '''GFP fusion:'''
 +
 +
* '''two-hybrid system:'''
  
 
* '''Antibody:'''
 
* '''Antibody:'''
  
 
=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
−
 
−
[[Josef Deutscher]], Paris-Grignon, France
 
−
 
−
[[Stülke|Jörg Stülke]], University of Göttingen, Germany [http://wwwuser.gwdg.de/~genmibio/stuelke.html Homepage]
 
  
 
=Your additional remarks=
 
=Your additional remarks=
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=References=
 
=References=
  
−
# 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]
−
# Frisby, D., and Zuber, P. 1994. Mutations in pts cause catabolite-resistant sporulation and altered regulation of spo0H in Bacillus subtilis. J. Bacteriol. 176: 2587-2595. [http://www.ncbi.nlm.nih.gov/sites/entrez/8169206  PubMed]
 
−
# Macek B, Mijakovic I, Olsen JV (2007) The serine/threonine/tyrosine phosphoproteome of the model bacterium Bacillus subtilis. ''Mol Cell Proteomics'' '''6(4):''' 697-707. [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed]
 

Revision as of 04:24, 12 April 2009

  • Description: unknown

Gene name ykwB
Synonyms
Essential no
Product unknown
Function unknown
MW, pI 19 kDa, 5.946
Gene length, protein length 519 bp, 173 aa
Immediate neighbours splB, mcpC
Gene sequence (+200bp) Protein sequence
Genetic context
YkwB 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: N-acetyltransferase domain
  • 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
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