Difference between revisions of "Sandbox"

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−
* '''Description:''' multidrug-efflux transporter <br/><br/>
+
* '''Description:''' cystathionine b-lyase <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'''
−
|''mdtP''
+
|''metC''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yusP ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yjcJ''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || multidrug-efflux transporter
+
|style="background:#ABCDEF;" align="center"| '''Product''' || cystathionine b-lyase
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || multidrug resistance
+
|style="background:#ABCDEF;" align="center"|'''Function''' || biosynthesis of methionine
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 57 kDa, 9.836  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 42 kDa, 5.757  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1623 bp, 541 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1170 bp, 390 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yusO]]'', ''[[yusQ]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[metI]]'', ''[[yjcK]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB15277&#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:CAB13045&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:yusP_context.gif]]
+
|-
 +
|-
 +
|colspan="2" | '''Genetic context''' <br/> [[Image:yjcJ_context.gif]]
 +
<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
 
|-
 
|-
 
|}
 
|}
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__TOC__
 
__TOC__
  
−
<br/><br/>
+
<br/><br/><br/><br/>
  
 
=The gene=
 
=The gene=
Line 34: Line 37:
 
=== Basic information ===
 
=== Basic information ===
  
−
* '''Locus tag:'''
+
* '''Locus tag:''' BSU11880
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
Line 40: Line 43:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' no entry
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yjcIJ.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG14028]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13163]
  
 
=== Additional information===
 
=== Additional information===
Line 51: Line 54:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:'''  
+
* '''Catalyzed reaction/ biological activity:''' L-cystathionine + H<sub>2</sub>O = L-homocysteine + NH<sub>3</sub> + pyruvate (according to Swiss-Prot)
  
−
* '''Protein family:''' EmrB family (according to Swiss-Prot)
+
* '''Protein family:''' trans-sulfuration enzymes family (according to Swiss-Prot)
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
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* '''Interactions:'''
 
* '''Interactions:'''
  
−
* '''Localization:''' cell membrane (according to Swiss-Prot),  membrane associated [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]
+
* '''Localization:''' cytoplasm (according to Swiss-Prot)
  
 
=== Database entries ===
 
=== Database entries ===
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* '''Structure:'''
 
* '''Structure:'''
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/O32182 O32182]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/O31632 O31632]
  
−
* '''KEGG entry:'''
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU11880]
  
−
* '''E.C. number:'''
+
* '''E.C. number:''' [http://www.expasy.org/enzyme/4.4.1.8 4.4.1.8]
  
 
=== Additional information===
 
=== Additional information===
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=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''[[mdtR]]-[[mdtP]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/19286808 PubMed]
+
* '''Operon:''' ''[[metI]]-[[metC]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/11832514 PubMed]
  
−
* '''[[Sigma factor]]:'''  
+
* '''Sigma factor:''' [[SigA]]  [http://www.ncbi.nlm.nih.gov/sites/entrez/11832514 PubMed]
  
−
* '''Regulation:'''
+
* '''Regulation:'''  
 +
**repressed by casamino acids [http://www.ncbi.nlm.nih.gov/pubmed/12107147 PubMed] 
 +
** induced by methionine starvation ([[S-box]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/10094622 PubMed]
  
−
* '''Regulatory mechanism:''' repression by [[MdtR]] [http://www.ncbi.nlm.nih.gov/sites/entrez/19286808 PubMed]
+
* '''Regulatory mechanism:''' [[S-box]]: transcription termination/ antitermination, the [[S-box]] [[riboswitch]] binds S-adenosylmethionine resulting in termination [http://www.ncbi.nlm.nih.gov/sites/entrez/10094622 PubMed]
  
 
* '''Additional information:'''
 
* '''Additional information:'''
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=Biological materials =
 
=Biological materials =
  
−
* '''Mutant:'''  
+
* '''Mutant:'''
  
 
* '''Expression vector:'''
 
* '''Expression vector:'''
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=References=
 
=References=
  
−
<pubmed>18763711 19286808, </pubmed>
+
<pubmed>12107147, </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]
+
# M&#228;der et al. (2002) Transcriptome and Proteome Analysis of ''Bacillus subtilis'' Gene Expression Modulated by Amino Acid Availability. ''J. Bacteriol'' '''184:''' 1844288-4295 [http://www.ncbi.nlm.nih.gov/pubmed/12107147 PubMed]
−
# Kim JY, Inaoka T, Hirooka K, Matsuoka H, Murata M, Ohki R, Adachi Y, Fujita Y, Ochi K (2009) Identification and characterization of a novel multidrug resistance operon ''mdtRP'' (''yusOP'') of ''Bacillus subtilis''. ''J. Bacteriol'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/19286808 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 13:24, 8 June 2009

  • Description: cystathionine b-lyase

Gene name metC
Synonyms yjcJ
Essential no
Product cystathionine b-lyase
Function biosynthesis of methionine
MW, pI 42 kDa, 5.757
Gene length, protein length 1170 bp, 390 aa
Immediate neighbours metI, yjcK
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
YjcJ context.gif
This image was kindly provided by SubtiList





The gene

Basic information

  • Locus tag: BSU11880

Phenotypes of a mutant

Database entries

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

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity: L-cystathionine + H2O = L-homocysteine + NH3 + pyruvate (according to Swiss-Prot)
  • Protein family: trans-sulfuration enzymes 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: cytoplasm (according to Swiss-Prot)

Database entries

  • Structure:
  • KEGG entry: [3]

Additional information

Expression and regulation

  • Regulation:
  • Regulatory mechanism: S-box: transcription termination/ antitermination, the S-box riboswitch binds S-adenosylmethionine resulting in termination PubMed
  • 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

Ulrike Mäder, Georg Homuth, Christian Scharf, Knut Büttner, Rüdiger Bode, Michael Hecker
Transcriptome and proteome analysis of Bacillus subtilis gene expression modulated by amino acid availability.
J Bacteriol: 2002, 184(15);4288-95
[PubMed:12107147] [WorldCat.org] [DOI] (P p)

  1. Mäder et al. (2002) Transcriptome and Proteome Analysis of Bacillus subtilis Gene Expression Modulated by Amino Acid Availability. J. Bacteriol 184: 1844288-4295 PubMed
  2. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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