Difference between revisions of "Sandbox"

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* '''Description:''' glucosamine-specific phosphotransferase system, EIICBA <br/><br/>
+
* '''Description:''' similar to L-alanoyl-D-glutamate peptidase <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'''
−
|''gamP''
+
|''cwlK''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ybfS, yzfA ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ycdD ''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || glucosamine-specific phosphotransferase system, EIICBA
+
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || glucosamine uptake and phosphorylation
+
|style="background:#ABCDEF;" align="center"|'''Function''' || cell wall turnover
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 67 kDa, 5.472  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 18 kDa, 5.66  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1893 bp, 631 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 501 bp, 167 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[gltP]]'', ''[[gamA]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ycdC]]'', ''[[rapJ]]''
 
|-
 
|-
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/gamP_nucleotide.txt    Gene sequence      (+200bp)  ]'''
+
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB12075&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/gamP_protein.txt Protein sequence]'''
 
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:gamP_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:ycdD_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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===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
−
 
−
delayed growth with glucosamine as the single carbon source [http://www.ncbi.nlm.nih.gov/sites/entrez/10627040 PubMed]
 
  
 
=== Database entries ===
 
=== Database entries ===
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* '''DBTBS entry:''' no entry
 
* '''DBTBS entry:''' no entry
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11014]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12760]
  
 
=== Additional information===
 
=== Additional information===
Line 57: Line 54:
 
* '''Catalyzed reaction/ biological activity:'''  
 
* '''Catalyzed reaction/ biological activity:'''  
  
−
* '''Protein family:''' PTS permease, glucose permease (Glc) family [http://www.ncbi.nlm.nih.gov/pubmed/10627040 PubMed]
+
* '''Protein family:'''
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
Line 75: Line 72:
 
* '''Interactions:'''
 
* '''Interactions:'''
  
−
* '''Localization:''' membrane associated [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]
+
* '''Localization:'''
  
 
=== Database entries ===
 
=== Database entries ===
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* '''Swiss prot entry:'''
 
* '''Swiss prot entry:'''
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU02350]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU02810]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
Line 91: Line 88:
 
=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''[[gamA]]-[[gamP]]''
+
* '''Operon:'''  
  
 
* '''[[Sigma factor]]:'''  
 
* '''[[Sigma factor]]:'''  
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* '''Regulatory mechanism:'''  
 
* '''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=
 +
 +
[[Ciaran Condon]], IBPC, Paris, France [http://www.ibpc.fr/UPR9073/condon/index_en.html Homepage]
  
 
=Your additional remarks=
 
=Your additional remarks=
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=References=
 
=References=
  
−
# 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]
+
# Fukushima T, Yao Y, Kitajima T, Yamamoto H, Sekiguchi J. (2007) Characterization of new L,D-endopeptidase gene product CwlK (previous YcdD) that hydrolyzes peptidoglycan in Bacillus subtilis. ''Mol Genet Genomics.'' '''Oct;278(4):''' 371-83. [http://www.ncbi.nlm.nih.gov/sites/entrez/17588176  PubMed]
−
# Hahne et al. (2008) From complementarity to comprehensiveness - targeting the membrane proteome of growing ''Bacillus subtilis'' by divergent approaches. Proteomics '''8:''' 4123-4136 [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]
 
−
# Reizer, J., Bachem, S., Reizer, A., Arnaud, M., Saier Jr., M. H. & Stülke, J. (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/sites/entrez/10627040 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 22:55, 28 April 2009

  • Description: similar to L-alanoyl-D-glutamate peptidase

Gene name cwlK
Synonyms ycdD
Essential no
Product unknown
Function cell wall turnover
MW, pI 18 kDa, 5.66
Gene length, protein length 501 bp, 167 aa
Immediate neighbours ycdC, rapJ
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
YcdD context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Coordinates:

Phenotypes of a mutant

Database entries

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

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:

Database entries

  • Structure:
  • Swiss prot entry:
  • 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

Ciaran Condon, IBPC, Paris, France Homepage

Your additional remarks

References

  1. Fukushima T, Yao Y, Kitajima T, Yamamoto H, Sekiguchi J. (2007) Characterization of new L,D-endopeptidase gene product CwlK (previous YcdD) that hydrolyzes peptidoglycan in Bacillus subtilis. Mol Genet Genomics. Oct;278(4): 371-83. PubMed
  2. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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