Difference between revisions of "Sandbox"

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Line 1: Line 1:
−
* '''Description:''' glucosaminidase <br/><br/>
+
* '''Description:''' similar to N-acetylmuramoyl-L-alanine amidase <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'''
−
|''lytD''
+
|''lytG''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''cwlG ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yubE''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || glucosaminidase
+
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || major autolysin, cell separation
+
|style="background:#ABCDEF;" align="center"|'''Function''' || cell wall turnover
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 95 kDa, 9.935  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 31 kDa, 8.277  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 2640 bp, 880 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 846 bp, 282 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[tagC]]'', ''[[pmi]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yubF]]'', ''[[yubD]]''
 
|-
 
|-
−
|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" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB15090&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:lytD_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:yubE_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:''' BSU35780
+
* '''Locus tag:''' BSU31120
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
Line 41: Line 41:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/lytD.html]
+
* '''DBTBS entry:''' no entry
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10455]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13954]
  
 
=== Additional information===
 
=== Additional information===
Line 52: Line 52:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''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)  
+
* '''Catalyzed reaction/ biological activity:''' Hydrolysis of 1,4-beta-linkages between N-acetyl-D-glucosamine and N-acetylmuramic acid residues in a peptidoglycan (according to Swiss-Prot)  
  
 
* '''Protein family:''' glycosyl hydrolase 73 family (according to Swiss-Prot)
 
* '''Protein family:''' glycosyl hydrolase 73 family (according to Swiss-Prot)
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* '''Interactions:'''
 
* '''Interactions:'''
  
−
* '''Localization:''' secreted (according to Swiss-Prot),  extracellular (signal peptide) [http://www.ncbi.nlm.nih.gov/pubmed/18957862 PubMed]
+
* '''Localization:''' secreted (according to Swiss-Prot)
  
 
=== Database entries ===
 
=== Database entries ===
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* '''Structure:'''
 
* '''Structure:'''
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P39848 P39848]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/O32083 O32083]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU35780]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU31120]
  
−
* '''E.C. number:''' [http://www.expasy.org/enzyme/3.2.1.96 3.2.1.96]
+
* '''E.C. number:'''
  
 
=== Additional information===
 
=== Additional information===
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=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''[[lytD]]''
+
* '''Operon:'''  
  
−
* '''[[Sigma factor]]:''' [[SigD]]
+
* '''[[Sigma factor]]:'''  
  
 
* '''Regulation:'''  
 
* '''Regulation:'''  
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* '''Regulatory mechanism:'''  
 
* '''Regulatory mechanism:'''  
  
−
* '''Additional information:'''
+
* '''Additional information:'''  
  
 
=Biological materials =
 
=Biological materials =
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=References=
 
=References=
  
−
<pubmed>18957862, </pubmed>
+
<pubmed>17427287, </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]
+
# Horsburgh GJ, Atrih A, Williamson MP, Foster SJ. (2006) Dimeric structure of the cell shape protein MreC and its functional implications. ''Mol Microbiol.'' '''Dec;62(6):''' 1631-42.  [http://www.ncbi.nlm.nih.gov/sites/entrez/17427287 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: similar to N-acetylmuramoyl-L-alanine amidase

Gene name lytG
Synonyms yubE
Essential no
Product unknown
Function cell wall turnover
MW, pI 31 kDa, 8.277
Gene length, protein length 846 bp, 282 aa
Immediate neighbours yubF, yubD
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
YubE context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Locus tag: BSU31120

Phenotypes of a mutant

Database entries

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

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity: Hydrolysis of 1,4-beta-linkages between N-acetyl-D-glucosamine and N-acetylmuramic acid residues in a peptidoglycan (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)

Database entries

  • Structure:
  • KEGG entry: [2]
  • 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

Fusinita van den Ent, Mark Leaver, Felipe Bendezu, Jeff Errington, Piet de Boer, Jan Löwe
Dimeric structure of the cell shape protein MreC and its functional implications.
Mol Microbiol: 2006, 62(6);1631-42
[PubMed:17427287] [WorldCat.org] [DOI] (P p)

  1. Horsburgh GJ, Atrih A, Williamson MP, Foster SJ. (2006) Dimeric structure of the cell shape protein MreC and its functional implications. Mol Microbiol. Dec;62(6): 1631-42. PubMed
  2. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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