Difference between revisions of "Sandbox"

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* '''Description:''' trigger enzyme: beta-glucoside-specific phosphotransferase system, EIIBC <br/><br/>
+
* '''Description:''' PTS, putative EIIC component <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'''
−
|''bglP''
+
|''ywbA''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''sytA ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ipa-16d ''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || trigger enzyme: beta-glucoside-specific phosphotransferase system, EIIBC
+
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || beta-glucoside uptake and phosphorylation, control of LicT activity
+
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 64 kDa, 6.809  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 47 kDa, 7.889  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1827 bp, 609 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1332 bp, 444 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[bglH]]'', ''[[yxxE]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ywbB]]'', ''[[epr]]''
 
|-
 
|-
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/bglP_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/ywbA_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/bglP_protein.txt Protein sequence]'''
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/ywbA_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:ywbA_context.gif]]
−
|-
 
−
|colspan="2" | '''Genetic context''' <br/> [[Image:bglP_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=
Line 44: Line 42:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/bglPH-yxiE.html]
+
* '''DBTBS entry:''' no entry
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10934]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10562]
  
 
=== Additional information===
 
=== Additional information===
Line 57: Line 55:
 
* '''Catalyzed reaction/ biological activity:'''  
 
* '''Catalyzed reaction/ biological activity:'''  
  
−
* '''Protein family:''' PTS permease, sucrose permease (Scr) family [http://www.ncbi.nlm.nih.gov/pubmed/10627040 PubMed]  
+
* '''Protein family:''' PTS permease, lactose permease (Lac) family [http://www.ncbi.nlm.nih.gov/pubmed/10627040 PubMed]  
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
Line 83: Line 81:
 
* '''Swiss prot entry:'''
 
* '''Swiss prot entry:'''
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU39270]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU38390]
  
−
* '''E.C. number:''' 2.7.1.69
+
* '''E.C. number:'''
  
 
=== Additional information===
 
=== Additional information===
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=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''[[bglP]]-[[bglH]]-[[yxiE]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/7883710 PubMed]
+
* '''Operon:'''  
  
−
* '''Sigma factor:''' [[SigA]]
+
* '''Sigma factor:'''  
  
−
* '''Regulation:''' repressed by glucose ([[CcpA]]) ,  induced by salicin  [http://www.ncbi.nlm.nih.gov/sites/entrez/7883710 PubMed], repressed by glucose (catabolite repression)
+
* '''Regulation:'''  
  
−
* '''Regulatory mechanism:''' [[CcpA]]: transcription repression,  Induction: [[LicT]]-dependent RNA switch (antitermination), catabolite repression: repression by [[CcpA]]  ([[CcpA]] binding site overlaps -35 region) and lack of [[LicT]]-dependent antitermination in the presence of gucose due to the requirement of [[LicT]] to be phosphorylated by [[PtsH| HPr]]
+
* '''Regulatory mechanism:'''  
  
−
* '''Additional information:'''
+
* '''Additional information:'''  
  
 
=Biological materials =
 
=Biological materials =
Line 122: Line 120:
  
 
# Reizer et al. (1999) Novel phosphotransferase system genes revealed by genome analysis - the complete complement of PTS proteins encoded within the genome of ''Bacillus subtilis''.  Microbiology '''145:''' 3419-3429 [http://www.ncbi.nlm.nih.gov/pubmed/10627040 PubMed]
 
# Reizer et al. (1999) Novel phosphotransferase system genes revealed by genome analysis - the complete complement of PTS proteins encoded within the genome of ''Bacillus subtilis''.  Microbiology '''145:''' 3419-3429 [http://www.ncbi.nlm.nih.gov/pubmed/10627040 PubMed]
−
 
−
# Le Coq, D., Lindner, C., Krüger, S., Steinmetz, M. & Stülke, J. (1995) New ß-glucosides (bgl) genes in ''Bacillus subtilis'': The ''bglP'' gene product has both transport and regulatory functions, similar to that of the ''Escherichia coli'' BglF protein. J. Bacteriol. 177: 1527-1535.  [http://www.ncbi.nlm.nih.gov/sites/entrez/7883710 PubMed]
 
−
# Krüger, S., Gertz, S. & Hecker, M. Transcriptional analysis of ''bglPH'' expression in ''Bacillus subtilis'': Evidence for two distinct pathways mediating carbon catabolite repression. J. Bacteriol. 178, 2637-2644 (1996). [http://www.ncbi.nlm.nih.gov/sites/entrez/8626332 PubMed]
 
−
# Krüger, S. and Hecker, M. (1995) Regulation of the putative ''bglPH'' operon for aryl-ß-glycoside utilization in ''Bacillus subtilis''. J. Bacteriol. 177, 5590-5597. [http://www.ncbi.nlm.nih.gov/sites/entrez/7559347 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 11:57, 6 April 2009

  • Description: PTS, putative EIIC component

Gene name ywbA
Synonyms ipa-16d
Essential no
Product unknown
Function unknown
MW, pI 47 kDa, 7.889
Gene length, protein length 1332 bp, 444 aa
Immediate neighbours ywbB, epr
Gene sequence (+200bp) Protein sequence
Genetic context
YwbA 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: PTS permease, lactose permease (Lac) family PubMed
  • 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:
  • 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. Reizer et al. (1999) Novel phosphotransferase system genes revealed by genome analysis - the complete complement of PTS proteins encoded within the genome of Bacillus subtilis. Microbiology 145: 3419-3429 PubMed
  2. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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