Difference between revisions of "Sandbox"

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−
* '''Description:''' thiaminase II <br/><br/>
+
* '''Description:''' RNA polymerase ECF-type [[sigma factor]] SigM <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'''
−
|''tenA''
+
|''sigM''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yhdM ''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || thiaminase II
+
|style="background:#ABCDEF;" align="center"| '''Product''' || RNA polymerase ECF-type [[sigma factor]] SigM
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || thiamine salvage
+
|style="background:#ABCDEF;" align="center"|'''Function''' || resistance against cell envelope stress, oxidative stress and salt stress
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 27 kDa, 4.99  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 19 kDa, 6.77  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 708 bp, 236 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 489 bp, 163 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yjbQ]]'', ''[[tenI]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yhdL]]'', ''[[yhdN]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB13022&#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:CAB12791&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:tenA_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:sigM_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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=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/tenAI-goxB-thiSGF-yjbV.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/sigM-yhdLK.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10791]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13019]
  
 
=== Additional information===
 
=== Additional information===
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* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
 +
 +
=== Genes/ operons controlled by SigM ===
 +
 +
''[[sigM]]-[[yhdL]]-[[yhdK]]'', ''[[yqjL]]'', ''[[ypbG]]'', ''[[ydaH]]'', ''[[ypuA]]'', ''[[radC]]'', ''[[yebC]]'', ''[[ywtF]]'', ''[[rodA]]'', ''[[ypuD]]'', ''[[ytpA]]'', ''[[ytpB]]'', ''[[yngC]]'', ''[[ycgR]]'', ''[[ycgQ]]''
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
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* '''Swiss prot entry:'''
 
* '''Swiss prot entry:'''
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU11650]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU09520]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
Line 88: Line 92:
 
=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:'''  
+
* '''Operon:''' ''[[sigM]]-[[yhdL]]-[[yhdK]]''
  
−
* '''[[Sigma factor]]:'''  
+
* '''[[Sigma factor]]:''' [[SigM]]
  
 
* '''Regulation:'''  
 
* '''Regulation:'''  
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* '''Regulatory mechanism:'''  
 
* '''Regulatory mechanism:'''  
  
−
* '''Additional information:'''  
+
* '''Additional information:'''
  
 
=Biological materials =
 
=Biological materials =
Line 113: Line 117:
  
 
=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
 +
[[John Helmann]], Cornell University, USA [http://www.micro.cornell.edu/research/labs/helmann-lab/index.cfm Homepage]
  
 
=Your additional remarks=
 
=Your additional remarks=

Revision as of 16:23, 25 April 2009

Gene name sigM
Synonyms yhdM
Essential no
Product RNA polymerase ECF-type sigma factor SigM
Function resistance against cell envelope stress, oxidative stress and salt stress
MW, pI 19 kDa, 6.77
Gene length, protein length 489 bp, 163 aa
Immediate neighbours yhdL, yhdN
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
SigM context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Coordinates:

Phenotypes of a mutant

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 SigM

sigM-yhdL-yhdK, yqjL, ypbG, ydaH, ypuA, radC, yebC, ywtF, rodA, ypuD, ytpA, ytpB, yngC, ycgR, ycgQ

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

  • Regulation:
  • Regulatory mechanism:
  • Additional information:

Biological materials

  • Mutant:
  • Expression vector:
  • lacZ fusion:
  • GFP fusion:
  • two-hybrid system:
  • Antibody:

Labs working on this gene/protein

John Helmann, Cornell University, USA Homepage

Your additional remarks

References

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