Difference between revisions of "Sandbox"

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−
* '''Description:''' trigger enzyme: lipoic acid synthetase and regulator of comE operon expression <br/><br/>
+
* '''Description:''' secretion of major autolysin LytC <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'''
−
|''lipA''
+
|''lytA''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yutB ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''lppX ''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || lipoic acid synthetase
+
|style="background:#ABCDEF;" align="center"| '''Product''' || secretion of major autolysin LytC
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || lipid metabolism
+
|style="background:#ABCDEF;" align="center"|'''Function''' || autolysis
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 33 kDa, 8.251  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 11 kDa, 4.061  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 894 bp, 298 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 306 bp, 102 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yutC]]'', ''[[lytH]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[lytB]]'', ''[[lytR]]''
 
|-
 
|-
−
|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" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB15581&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:lipA_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:lytA_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:''' BSU32330
+
* '''Locus tag:''' BSU35640
  
 
===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 ===
  
−
* '''DBTBS entry:''' no entry
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/lytABC.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG14038]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10405]
  
 
=== Additional information===
 
=== Additional information===
Line 54: Line 52:
 
=== Basic information/ Evolution ===
 
=== 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 + 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]
+
* '''Catalyzed reaction/ biological activity:'''  
  
−
* '''Protein family:''' Lipoyl synthase family (according to Swiss-Prot) AB hydrolase superfamily (according to Swiss-Prot)
+
* '''Protein family:'''
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
Line 74: Line 72:
 
* '''Interactions:'''
 
* '''Interactions:'''
  
−
* '''Localization:''' extracellular (signal peptide) [http://www.ncbi.nlm.nih.gov/pubmed/18957862 PubMed]
+
* '''Localization:''' cell membrane (according to Swiss-Prot)
  
 
=== Database entries ===
 
=== Database entries ===
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* '''Structure:'''
 
* '''Structure:'''
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/O32129 O32129]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/Q02112 Q02112]
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU32330]
+
 
 +
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU35640]
  
−
* '''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:'''  
+
* '''Operon:''' ''[[lytA]]-[[lytB]]-[[lytC]]''
  
−
* '''Sigma factor:'''  
+
* '''[[Sigma factor]]:''' [[SigA]], [[SigD]]
  
 
* '''Regulation:'''  
 
* '''Regulation:'''  
  
−
* '''Regulatory mechanism:'''  
+
* '''Regulatory mechanism:''' repressed by [[YvrHb]]  [http://www.ncbi.nlm.nih.gov/sites/entrez/16306698 PubMed]
  
−
* '''Additional information:'''  
+
* '''Additional information:'''
  
 
=Biological materials =
 
=Biological materials =
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=References=
 
=References=
  
−
<pubmed>18957862 19028902, </pubmed>
+
<pubmed>16306698, </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]
+
# Serizawa M, Kodama K, Yamamoto H, Kobayashi K, Ogasawara N, Sekiguchi J. (2005) Functional analysis of the YvrGHb two-component system of ''Bacillus subtilis'': identification of the regulated genes by DNA microarray and northern blot analyses. ''Biosci. Biotechnol. Biochem.'' '''69:''' 2155-2169. [http://www.ncbi.nlm.nih.gov/sites/entrez/16306698 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]
 
 
# 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 13:23, 8 June 2009

  • Description: secretion of major autolysin LytC

Gene name lytA
Synonyms lppX
Essential no
Product secretion of major autolysin LytC
Function autolysis
MW, pI 11 kDa, 4.061
Gene length, protein length 306 bp, 102 aa
Immediate neighbours lytB, lytR
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
LytA context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Locus tag: BSU35640

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:
  • Paralogous protein(s):

Extended information on the protein

  • Kinetic information:
  • Domains:
  • Modification:
  • Cofactor(s):
  • Effectors of protein activity:
  • Interactions:
  • Localization: cell membrane (according to Swiss-Prot)

Database entries

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

Additional information

Expression and regulation

  • 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

Masakuni Serizawa, Keisuke Kodama, Hiroki Yamamoto, Kazuo Kobayashi, Naotake Ogasawara, Junichi Sekiguchi
Functional analysis of the YvrGHb two-component system of Bacillus subtilis: identification of the regulated genes by DNA microarray and northern blot analyses.
Biosci Biotechnol Biochem: 2005, 69(11);2155-69
[PubMed:16306698] [WorldCat.org] [DOI] (P p)

  1. Serizawa M, Kodama K, Yamamoto H, Kobayashi K, Ogasawara N, Sekiguchi J. (2005) Functional analysis of the YvrGHb two-component system of Bacillus subtilis: identification of the regulated genes by DNA microarray and northern blot analyses. Biosci. Biotechnol. Biochem. 69: 2155-2169. PubMed
  2. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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