Difference between revisions of "Sandbox"

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* '''Description:''' inhibitor of AbrB activity<br/><br/>
+
* '''Description:''' cell wall hydrolase (major autolysin),endopeptidase-type autolysin <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'''
|''abbA ''
+
|''lytE''
 
|-
 
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ykzF''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''papQ, cwlF ''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || anti-repressor
+
|style="background:#ABCDEF;" align="center"| '''Product''' || cell wall hydrolase (major autolysin),endopeptidase-type autolysin
 
|-
 
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || inhibition of AbrB
+
|style="background:#ABCDEF;" align="center"|'''Function''' || major autolysin, cell separation, cell lysis
 
|-
 
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 7 kDa, 4.642  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 37 kDa, 10.713  
 
|-
 
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 195 bp, 65 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1029 bp, 343 aa  
 
|-
 
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ykuK]]'', ''[[ykuL]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[phoA]]'', ''[[citR]]''
 
|-
 
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB13285&#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:CAB12781&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
|colspan="2" | '''Genetic context''' <br/> [[Image:ykzF_context.gif]]
+
|-
 +
|-
 +
|colspan="2" | '''Genetic context''' <br/> [[Image:lytE_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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=== Database entries ===
 
=== Database entries ===
  
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ykuJK-ykzF-ykuL-ccpC.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/lytE.html]
  
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13334]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11406]
  
 
=== Additional information===
 
=== Additional information===
Line 52: Line 54:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
* '''Catalyzed reaction/ biological activity:''' inhibition of AbrB activity [http://www.ncbi.nlm.nih.gov/sites/entrez/18840696 PubMed]
+
* '''Catalyzed reaction/ biological activity:'''  
  
 
* '''Protein family:'''
 
* '''Protein family:'''
Line 70: Line 72:
 
* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
  
* '''Interactions:''' [[AbbA]]-[[AbrB]], AbbA-[[AbrB]] [http://www.ncbi.nlm.nih.gov/sites/entrez/18840696 PubMed]
+
* '''Interactions:''' [[MreBH]]-[[LytE]],  
  
 
* '''Localization:'''
 
* '''Localization:'''
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* '''Swiss prot entry:'''
 
* '''Swiss prot entry:'''
  
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU14120]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU09420]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
Line 90: Line 92:
 
* '''Operon:'''  
 
* '''Operon:'''  
  
* '''Sigma factor:'''  
+
* '''[[Sigma factor]]:'''  
  
* '''Regulation:''' repressed by glucose (4.3-fold) ([[CcpA]]) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed],  subject to carbon catabolite repression (4-fold: [[CcpA]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/12850135 PubMed], expressed at onset of stationary phase ([[Spo0A]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/18840696 PubMed]
+
* '''Regulation:'''  
  
* '''Regulatory mechanism:''' [[CcpA]]: transcription repression,  [[CcpA]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/12850135 PubMed], [[Spo0A]]: transcription activation by Spo0A~P [http://www.ncbi.nlm.nih.gov/sites/entrez/18840696 PubMed]
+
* '''Regulatory mechanism:'''  
  
* '''Additional information:'''
+
* '''Additional information:'''  
  
 
=Biological materials =
 
=Biological materials =
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=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
 
[[Richard Losick]], Harvard Univ., Cambridge, USA [http://www.mcb.harvard.edu/Losick/ 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]
+
# Carballido-Lopez, R., Formstone, A., Li, Y., Ehrlich, S. D., and Errington, J. (2006) Actin homolog MreBH governs cell morphogenesis by localization of the cell wall hydrolase LytE. Dev. Cell 11: 399-409.[http://www.ncbi.nlm.nih.gov/sites/entrez/16950129 PubMed]
# Banse et al. (2008) Parallel pathways of repression and antirepression governing the transition to stationary phase in ''Bacillus subtilis''.''Proc. Natl. Acad. Sci. USA'' '''105:''' 15547-15552. [http://www.ncbi.nlm.nih.gov/sites/entrez/18840696 PubMed]
 
# Blencke, H.-M., Homuth, G., Ludwig, H., Mäder, U., Hecker, M. & Stülke, J. (2003) Transcriptional profiling of gene expression in response to glucose in Bacillus subtilis: regulation of the central metabolic pathways. Metab. Engn. 5: 133-149. [http://www.ncbi.nlm.nih.gov/sites/entrez/12850135 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 00:00, 28 April 2009

  • Description: cell wall hydrolase (major autolysin),endopeptidase-type autolysin

Gene name lytE
Synonyms papQ, cwlF
Essential no
Product cell wall hydrolase (major autolysin),endopeptidase-type autolysin
Function major autolysin, cell separation, cell lysis
MW, pI 37 kDa, 10.713
Gene length, protein length 1029 bp, 343 aa
Immediate neighbours phoA, citR
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
LytE context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Coordinates:

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:
  • Localization:

Database entries

  • Structure:
  • Swiss prot entry:
  • KEGG entry: [3]
  • 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. Carballido-Lopez, R., Formstone, A., Li, Y., Ehrlich, S. D., and Errington, J. (2006) Actin homolog MreBH governs cell morphogenesis by localization of the cell wall hydrolase LytE. Dev. Cell 11: 399-409.PubMed
  2. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed