Difference between revisions of "Sandbox"

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−
* '''Description:''' malic enzyme <br/><br/>
+
* '''Description:''' transcriptional activator of the mannose operon <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'''
−
|''maeA''  
+
|''manR''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ywkA ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yjdC ''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || NAD-dependent malate dehydrogenase
+
|style="background:#ABCDEF;" align="center"| '''Product''' || transcriptional activator (PRD protein)
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || malate utilization
+
|style="background:#ABCDEF;" align="center"|'''Function''' || regulation of mannose utilization
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 63 kDa, 4.883  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 75 kDa, 8.04  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1746 bp, 582 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1944 bp, 648 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ywkB]]'', ''[[tdk]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yjdB]]'', ''[[manP]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB15722&#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:CAB13057&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:ywkA_context.gif]]
+
|-
 +
|-
 +
|colspan="2" | '''Genetic context''' <br/> [[Image:manR_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:''' BSU37050
+
* '''Locus tag:''' BSU12000
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
Line 41: Line 43:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ywkAB.html]
+
* '''DBTBS entry:''' no entry
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11312]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13175]
  
 
=== Additional information===
 
=== Additional information===
Line 52: Line 54:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:''' (S)-malate + NAD<sup>+</sup> = pyruvate + CO<sub>2</sub> + NADH (according to Swiss-Prot) malate --> pyruvate
+
* '''Catalyzed reaction/ biological activity:'''  
  
−
* '''Protein family:''' malic enzymes family (according to Swiss-Prot)
+
* '''Protein family:'''
  
−
* '''Paralogous protein(s):''' [[MalS]]
+
* '''Paralogous protein(s):'''
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
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* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
  
−
* '''Interactions:'''
+
* '''Interactions:''' [[ManP]]-[[ManR]],  [[PtsH]]-[[ManR]],
  
 
* '''Localization:'''
 
* '''Localization:'''
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* '''Structure:'''
 
* '''Structure:'''
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P45868 P45868]
+
* '''Swiss prot entry:'''
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU37050]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU12000]
  
−
* '''E.C. number:''' [http://www.expasy.org/enzyme/1.1.1.38 1.1.1.38]
+
* '''E.C. number:'''
  
 
=== Additional information===
 
=== Additional information===
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=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''[[maeA]]''-''[[ywkB]]''
+
* '''Operon:'''  
  
−
* '''Sigma factor:''' [[SigA]]
+
* '''[[Sigma factor]]:'''  
  
−
* '''Regulation:''' induced by malate ([[MalR]])
+
* '''Regulation:'''  
  
−
* '''Regulatory mechanism:''' [[MalR]]: transcription activation
+
* '''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=
−
 
−
[[Stephane Aymerich |Stephane Aymerich]], Microbiology and Molecular Genetics, INRA Paris-Grignon, France
 
  
 
=Your additional remarks=
 
=Your additional remarks=
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=References=
 
=References=
  
−
<pubmed>12949160, </pubmed>
+
<pubmed>10627040 10627040, </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 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]
 +
# 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 13:23, 8 June 2009

  • Description: transcriptional activator of the mannose operon

Gene name manR
Synonyms yjdC
Essential no
Product transcriptional activator (PRD protein)
Function regulation of mannose utilization
MW, pI 75 kDa, 8.04
Gene length, protein length 1944 bp, 648 aa
Immediate neighbours yjdB, manP
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
ManR context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Locus tag: BSU12000

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:
  • 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

Your additional remarks

References

Jonathan Reizer, Steffi Bachem, Aiala Reizer, Maryvonne Arnaud, Milton H Saier, Jörg Stülke
Novel phosphotransferase system genes revealed by genome analysis - the complete complement of PTS proteins encoded within the genome of Bacillus subtilis.
Microbiology (Reading): 1999, 145 ( Pt 12);3419-3429
[PubMed:10627040] [WorldCat.org] [DOI] (P p)

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