Difference between revisions of "Sandbox"

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* '''Description:''' heptaprenyl diphosphate synthase component I <br/><br/>
+
* '''Description:''' trigger enzyme: lichenan-specific phosphotransferase system, EIIB 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'''
−
|''hepS''
+
|''licB''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''gerCA, hepA ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''celA ''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
+
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || heptaprenyl diphosphate synthase component I
+
|style="background:#ABCDEF;" align="center"| '''Product''' || trigger enzyme: lichenan-specific <br/>phosphotransferase system, EIIB component
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || menaquinone biosynthesis
+
|style="background:#ABCDEF;" align="center"|'''Function''' || lichenan uptake and phosphorylation,  <br/>control of LicR activity
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 28 kDa, 6.273  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 10 kDa, 6.314  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 753 bp, 251 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 306 bp, 102 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[menH]]'', ''[[mtrB]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[licC]]'', ''[[licR]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB14192&#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:CAB15885&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:hepS_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:licB_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 38: Line 38:
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
−
 
−
essential [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
 
  
 
=== Database entries ===
 
=== Database entries ===
Line 45: Line 43:
 
* '''DBTBS entry:''' no entry
 
* '''DBTBS entry:''' no entry
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10279]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11347]
  
 
=== Additional information===
 
=== Additional information===
Line 56: Line 54:
 
* '''Catalyzed reaction/ biological activity:'''  
 
* '''Catalyzed reaction/ biological activity:'''  
  
−
* '''Protein family:'''
+
* '''Protein family:''' PTS permease, lactose permease (Lac) family [http://www.ncbi.nlm.nih.gov/pubmed/10627040 PubMed]
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
Line 66: Line 64:
 
* '''Domains:'''  
 
* '''Domains:'''  
  
−
* '''Modification:'''
+
* '''Modification:''' phosphorylation on Ser-37 [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed]
  
 
* '''Cofactor(s):'''
 
* '''Cofactor(s):'''
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* '''Swiss prot entry:'''
 
* '''Swiss prot entry:'''
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU22760]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU38590]
  
−
* '''E.C. number:'''
+
* '''E.C. number:''' 2.7.1.69
  
 
=== Additional information===
 
=== Additional information===
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=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:'''  
+
* '''Operon:''' ''[[licB]]-[[licC]]-[[licA]]-[[licH]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/8990303 PubMed]
  
−
* '''[[Sigma factor]]:'''  
+
* '''[[Sigma factor]]:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/8990303 PubMed]
  
−
* '''Regulation:'''  
+
* '''Regulation:''' repressed by glucose ([[CcpA]]) ,  carbon catabolite repression, induction by oligomeric ß-glucosides [http://www.ncbi.nlm.nih.gov/sites/entrez/8990303 PubMed]
  
−
* '''Regulatory mechanism:'''  
+
* '''Regulatory mechanism:''' [[CcpA]]: transcription repression,  catabolite repression: repression by [[CcpA]], induction: transcription activation by the PRD-type regulator [[LicR]] [http://www.ncbi.nlm.nih.gov/sites/entrez/8990303 PubMed]
  
−
* '''Additional information:'''  
+
* '''Additional information:'''
  
 
=Biological materials =
 
=Biological materials =
Line 120: Line 118:
 
=References=
 
=References=
  
 +
# 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]
 +
 +
# Macek et al. (2007) The serine/ threonine/ tyrosine phosphoproteome of the model  bacterium ''Bacillus subtilis''. Mol. Cell. Proteomics 6: 697-707  [http://www.ncbi.nlm.nih.gov/pubmed/17218307 PubMed]
 +
# Tobisch, S., P. Glaser, S. Krüger, and M. Hecker. 1997. Identification and characterization of a new ß-glucoside utilization system in ''Bacillus subtilis''. J. Bacteriol. 179:496-506. [http://www.ncbi.nlm.nih.gov/sites/entrez/8990303 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 13:32, 25 April 2009

  • Description: trigger enzyme: lichenan-specific phosphotransferase system, EIIB component

Gene name licB
Synonyms celA
Essential no
Product trigger enzyme: lichenan-specific
phosphotransferase system, EIIB component
Function lichenan uptake and phosphorylation,
control of LicR activity
MW, pI 10 kDa, 6.314
Gene length, protein length 306 bp, 102 aa
Immediate neighbours licC, licR
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
LicB 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: phosphorylation on Ser-37 PubMed
  • Cofactor(s):
  • Effectors of protein activity:
  • Interactions:
  • Localization:

Database entries

  • Structure:
  • Swiss prot entry:
  • KEGG entry: [2]
  • E.C. number: 2.7.1.69

Additional information

Expression and regulation

  • Regulation: repressed by glucose (CcpA) , carbon catabolite repression, induction by oligomeric ß-glucosides PubMed
  • Regulatory mechanism: CcpA: transcription repression, catabolite repression: repression by CcpA, induction: transcription activation by the PRD-type regulator LicR PubMed
  • 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
  1. Macek et al. (2007) The serine/ threonine/ tyrosine phosphoproteome of the model bacterium Bacillus subtilis. Mol. Cell. Proteomics 6: 697-707 PubMed
  2. Tobisch, S., P. Glaser, S. Krüger, and M. Hecker. 1997. Identification and characterization of a new ß-glucoside utilization system in Bacillus subtilis. J. Bacteriol. 179:496-506. PubMed
  3. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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