Difference between revisions of "Sandbox"

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−
* '''Description:''' secretion of major autolysin LytC <br/><br/>
+
* '''Description:''' glucosaminidase <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'''
−
|''lytA''
+
|''lytD''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''lppX ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''cwlG ''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || secretion of major autolysin LytC
+
|style="background:#ABCDEF;" align="center"| '''Product''' || glucosaminidase
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || autolysis
+
|style="background:#ABCDEF;" align="center"|'''Function''' || major autolysin, cell separation
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 11 kDa, 4.061  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 95 kDa, 9.935  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 306 bp, 102 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 2640 bp, 880 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[lytB]]'', ''[[lytR]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[tagC]]'', ''[[pmi]]''
 
|-
 
|-
−
|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" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB15595&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:lytA_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:lytD_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:''' BSU35640
+
* '''Locus tag:''' BSU35780
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
Line 41: Line 41:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/lytABC.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/lytD.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10405]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10455]
  
 
=== Additional information===
 
=== Additional information===
Line 52: Line 52:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:'''  
+
* '''Catalyzed reaction/ biological activity:''' Endohydrolysis of the N,N'-diacetylchitobiosyl unit in high-mannose glycopeptides and glycoproteins containing the -(Man(GlcNAc)<sub>2</sub>)Asn-structure (according to Swiss-Prot)
  
−
* '''Protein family:'''
+
* '''Protein family:''' glycosyl hydrolase 73 family (according to Swiss-Prot)
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
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* '''Interactions:'''
 
* '''Interactions:'''
  
−
* '''Localization:''' cell membrane (according to Swiss-Prot)
+
* '''Localization:''' secreted (according to Swiss-Prot),  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/Q02112 Q02112]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P39848 P39848]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU35640]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU35780]
  
−
* '''E.C. number:'''
+
* '''E.C. number:''' [http://www.expasy.org/enzyme/3.2.1.96 3.2.1.96]
  
 
=== Additional information===
 
=== Additional information===
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=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''[[lytA]]-[[lytB]]-[[lytC]]''
+
* '''Operon:''' ''[[lytD]]''
  
−
* '''[[Sigma factor]]:''' [[SigA]], [[SigD]]
+
* '''[[Sigma factor]]:''' [[SigD]]
  
 
* '''Regulation:'''  
 
* '''Regulation:'''  
  
−
* '''Regulatory mechanism:''' repressed by [[YvrHb]]  [http://www.ncbi.nlm.nih.gov/sites/entrez/16306698 PubMed]
+
* '''Regulatory mechanism:'''  
  
 
* '''Additional information:'''
 
* '''Additional information:'''
Line 118: Line 118:
 
=References=
 
=References=
  
−
<pubmed>16306698, </pubmed>
+
<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]
+
# 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]
 
# 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: glucosaminidase

Gene name lytD
Synonyms cwlG
Essential no
Product glucosaminidase
Function major autolysin, cell separation
MW, pI 95 kDa, 9.935
Gene length, protein length 2640 bp, 880 aa
Immediate neighbours tagC, pmi
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
LytD context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Locus tag: BSU35780

Phenotypes of a mutant

Database entries

  • DBTBS entry: [1]
  • SubtiList entry: [2]

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity: Endohydrolysis of the N,N'-diacetylchitobiosyl unit in high-mannose glycopeptides and glycoproteins containing the -(Man(GlcNAc)2)Asn-structure (according to Swiss-Prot)
  • Protein family: glycosyl hydrolase 73 family (according to Swiss-Prot)
  • Paralogous protein(s):

Extended information on the protein

  • Kinetic information:
  • Domains:
  • Modification:
  • Cofactor(s):
  • Effectors of protein activity:
  • Interactions:
  • Localization: secreted (according to Swiss-Prot), extracellular (signal peptide) PubMed

Database entries

  • Structure:
  • KEGG entry: [3]

Additional information

Expression and regulation

  • 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

Birgit Voigt, Haike Antelmann, Dirk Albrecht, Armin Ehrenreich, Karl-Heinz Maurer, Stefan Evers, Gerhard Gottschalk, Jan Maarten van Dijl, Thomas Schweder, Michael Hecker
Cell physiology and protein secretion of Bacillus licheniformis compared to Bacillus subtilis.
J Mol Microbiol Biotechnol: 2009, 16(1-2);53-68
[PubMed:18957862] [WorldCat.org] [DOI] (I p)

  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. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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