Difference between revisions of "Sandbox"

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−
* '''Description:''' maltose-specific phosphotransferase system, EIICB <br/><br/>
+
* '''Description:''' two-component response regulator, regulation of malate uptake <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'''
−
|''malP''
+
|''malR''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''glvC''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yufM''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || maltose-specific phosphotransferase system, EIICB
+
|style="background:#ABCDEF;" align="center"| '''Product''' || two-component response regulator
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || maltose uptake and phosphorylation
+
|style="background:#ABCDEF;" align="center"|'''Function''' || regulation of malate uptake
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 57 kDa, 8.872  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 26 kDa, 5.976  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1581 bp, 527 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 705 bp, 235 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[glvR]]'', ''[[yfiB]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[malK]]'', ''[[yufN]]''
 
|-
 
|-
 
|colspan="2" style="background:#FAF8CC;" align="center"|'''Hier soll was neues rein'''
 
|colspan="2" style="background:#FAF8CC;" align="center"|'''Hier soll was neues rein'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:malP_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:yufM_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>
 
|-
 
|-
Line 39: Line 39:
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
  
−
no growth on maltose as single carbon source [http://www.ncbi.nlm.nih.gov/sites/entrez/10627040 PubMed]
+
unable to use malate as the single carbon source [http://www.ncbi.nlm.nih.gov/sites/entrez/12949159 PubMed]
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' no entry
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yufM.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11848]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12348]
  
 
=== Additional information===
 
=== Additional information===
Line 56: Line 56:
 
* '''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):'''
 +
 +
=== Genes/ operons controlled by MalR ===
 +
''[[maeN]]'', ''[[yflS]]'', ''[[ywkA]]''
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
Line 82: Line 85:
 
* '''Swiss prot entry:'''
 
* '''Swiss prot entry:'''
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU08200]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU31530]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
Line 90: Line 93:
 
=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''[[malA]]-[[glvR]]-[[malP]]''
+
* '''Operon:'''  
  
−
* '''[[Sigma factor]]:''' [[SigA]]
+
* '''[[Sigma factor]]:'''  
  
−
* '''Regulation:''' repressed by glucose ([[CcpA]]) 
+
* '''Regulation:'''  
  
−
* '''Regulatory mechanism:''' [[CcpA]]: transcription repression
+
* '''Regulatory mechanism:'''  
  
−
* '''Additional information:'''
+
* '''Additional information:'''  
  
 
=Biological materials =
 
=Biological materials =
Line 115: Line 118:
  
 
=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
 +
 +
[[Stephane Aymerich |Stephane Aymerich]], Microbiology and Molecular Genetics, INRA Paris-Grignon, France
  
 
=Your additional remarks=
 
=Your additional remarks=
Line 120: Line 125:
 
=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]
+
# Tanaka, K., K. Kobayashi, and N. Ogasawara. 2003. The Bacillus subtilis YufLM two-component system regulates the expression of the malate transporters MaeN (YufR) and YflS, and is essential for utilization of malate in minimal medium. Microbiology 149: 2317-2329. [http://www.ncbi.nlm.nih.gov/sites/entrez/12949159 PubMed]
−
 
+
# Doan, T., P. Servant, S. Tojo, H. Yamaguchi, G. Lerondel, K. Yoshida, Y. Fujita, and S. Aymerich. 2003. The Bacillus subtilis ywkA gene encodes a malic enzyme and its transcription is activated by the YufL/YufM two-component system in response to malate. Microbiology 149: 2331-2343. [http://www.ncbi.nlm.nih.gov/sites/entrez/12949160 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 20:47, 15 April 2009

  • Description: two-component response regulator, regulation of malate uptake

Gene name malR
Synonyms yufM
Essential no
Product two-component response regulator
Function regulation of malate uptake
MW, pI 26 kDa, 5.976
Gene length, protein length 705 bp, 235 aa
Immediate neighbours malK, yufN
Hier soll was neues rein
Genetic context
YufM context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Coordinates:

Phenotypes of a mutant

unable to use malate as the single carbon source PubMed

Database entries

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

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity:
  • Protein family:
  • Paralogous protein(s):

Genes/ operons controlled by MalR

maeN, yflS, ywkA

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: [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

Stephane Aymerich, Microbiology and Molecular Genetics, INRA Paris-Grignon, France

Your additional remarks

References

  1. Tanaka, K., K. Kobayashi, and N. Ogasawara. 2003. The Bacillus subtilis YufLM two-component system regulates the expression of the malate transporters MaeN (YufR) and YflS, and is essential for utilization of malate in minimal medium. Microbiology 149: 2317-2329. PubMed
  2. Doan, T., P. Servant, S. Tojo, H. Yamaguchi, G. Lerondel, K. Yoshida, Y. Fujita, and S. Aymerich. 2003. The Bacillus subtilis ywkA gene encodes a malic enzyme and its transcription is activated by the YufL/YufM two-component system in response to malate. Microbiology 149: 2331-2343. PubMed
  3. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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