Difference between revisions of "Sandbox"

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* '''Description:''' lichenan-specific phosphotransferase system, EIIC component <br/><br/>
+
* '''Description:''' trigger enzyme: lipoic acid synthetase and regulator of comE operon expression <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'''
−
|''licC''
+
|''lipA''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''celB ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yutB ''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || lichenan-specific phosphotransferase system, <br/>EIIC component
+
|style="background:#ABCDEF;" align="center"| '''Product''' || lipoic acid synthetase
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || lichenan uptake and phosphorylation
+
|style="background:#ABCDEF;" align="center"|'''Function''' || lipid metabolism
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 48 kDa, 8.584  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 33 kDa, 8.251  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1356 bp, 452 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 894 bp, 298 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[licA]]'', ''[[licB]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yutC]]'', ''[[lytH]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB15884&#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:CAB15223&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:licC_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:lipA_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/>
  
 
=The gene=
 
=The gene=
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=== Basic information ===
 
=== Basic information ===
  
−
* '''Locus tag:''' BSU38580
+
* '''Locus tag:''' BSU32330
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
 +
 +
reduced transformation efficiency [http://www.ncbi.nlm.nih.gov/sites/entrez/19028902 PubMed]
  
 
=== Database entries ===
 
=== Database entries ===
Line 43: Line 45:
 
* '''DBTBS entry:''' no entry
 
* '''DBTBS entry:''' no entry
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11348]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG14038]
  
 
=== Additional information===
 
=== Additional information===
Line 52: Line 54:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:'''  
+
* '''Catalyzed reaction/ biological activity:''' Protein N(6)-(octanoyl)lysine + 2 sulfur + 2 S-adenosyl-L-methionine = protein N(6)-(lipoyl)lysine + 2 L-methionine + 2 5'-deoxyadenosine (according to Swiss-Prot) Triacylglycerol + H<sub>2</sub>O = diacylglycerol + a carboxylate (according to Swiss-Prot) required for ''[[comEA]]'' transcription  [http://www.ncbi.nlm.nih.gov/sites/entrez/19028902 PubMed]
  
−
* '''Protein family:''' PTS permease, lactose permease (Lac) family [http://www.ncbi.nlm.nih.gov/pubmed/10627040 PubMed]
+
* '''Protein family:''' Lipoyl synthase family (according to Swiss-Prot) AB hydrolase superfamily (according to Swiss-Prot)
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
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* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
  
−
* '''Interactions:''' [[LicB]]-[[LicC]]
+
* '''Interactions:'''
  
−
* '''Localization:''' cell membrane (according to Swiss-Prot)
+
* '''Localization:''' extracellular (signal peptide) [http://www.ncbi.nlm.nih.gov/pubmed/18957862 PubMed]
  
 
=== Database entries ===
 
=== Database entries ===
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* '''Structure:'''
 
* '''Structure:'''
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P46317 P46317]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/O32129 O32129]
 +
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU32330]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU38580]
+
* '''E.C. number:''' [http://www.expasy.org/enzyme/2.8.1.8 2.8.1.8] 3.1.1.3]
−
 
 
−
* '''E.C. number:'''
 
  
 
=== Additional information===
 
=== Additional information===
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=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''[[licB]]-[[licC]]-[[licA]]-[[licH]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/8990303 PubMed]
+
* '''Operon:'''  
  
−
* '''[[Sigma factor]]:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/8990303 PubMed]
+
* '''Sigma factor:'''  
  
−
* '''Regulation:''' repressed by glucose ([[CcpA]]) ,  carbon catabolite repression, induction by oligomeric ß-glucosides [http://www.ncbi.nlm.nih.gov/sites/entrez/8990303 PubMed]
+
* '''Regulation:'''  
  
−
* '''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]
+
* '''Regulatory mechanism:'''  
  
−
* '''Additional information:'''
+
* '''Additional information:'''  
  
 
=Biological materials =
 
=Biological materials =
Line 118: Line 119:
 
=References=
 
=References=
  
−
<pubmed>10627040 8990303, </pubmed>
+
<pubmed>18957862 19028902, </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]
+
# 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]
−
 
+
# Ogura, M. and T. Tanaka (2009) The ''Bacillus subtilis'' Late Competence Operon ''comE'' Is Transcriptionally Regulated by ''yutB'' and under Post-Transcription Initiation Control by ''comN'' (''yrzD'') ''J. Bacteriol.'' '''191:''' 949-958. [http://www.ncbi.nlm.nih.gov/sites/entrez/19028902 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 13:22, 8 June 2009

  • Description: trigger enzyme: lipoic acid synthetase and regulator of comE operon expression

Gene name lipA
Synonyms yutB
Essential no
Product lipoic acid synthetase
Function lipid metabolism
MW, pI 33 kDa, 8.251
Gene length, protein length 894 bp, 298 aa
Immediate neighbours yutC, lytH
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
LipA context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Locus tag: BSU32330

Phenotypes of a mutant

reduced transformation efficiency PubMed

Database entries

  • DBTBS entry: no entry
  • SubtiList entry: [1]

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity: Protein N(6)-(octanoyl)lysine + 2 sulfur + 2 S-adenosyl-L-methionine = protein N(6)-(lipoyl)lysine + 2 L-methionine + 2 5'-deoxyadenosine (according to Swiss-Prot) Triacylglycerol + H2O = diacylglycerol + a carboxylate (according to Swiss-Prot) required for comEA transcription PubMed
  • Protein family: Lipoyl synthase family (according to Swiss-Prot) AB hydrolase 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: extracellular (signal peptide) PubMed

Database entries

  • Structure:

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. 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. Ogura, M. and T. Tanaka (2009) The Bacillus subtilis Late Competence Operon comE Is Transcriptionally Regulated by yutB and under Post-Transcription Initiation Control by comN (yrzD) J. Bacteriol. 191: 949-958. PubMed
  3. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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