Difference between revisions of "Sandbox"

From SubtiWiki
Jump to: navigation, search
Line 1: Line 1:
* '''Description:''' RNA polymerase ECF-type [[sigma factor]] SigM <br/><br/>
+
* '''Description:''' aliphatic sulfonate monooxygenase <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'''
|''sigM''
+
|''ssuD''
 
|-
 
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yhdM ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ygcA, yzeC ''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || RNA polymerase ECF-type [[sigma factor]] SigM
+
|style="background:#ABCDEF;" align="center"| '''Product''' || aliphatic sulfonate monooxygenase
 
|-
 
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || resistance against cell envelope stress, oxidative stress and salt stress
+
|style="background:#ABCDEF;" align="center"|'''Function''' || sulfonate reduction
 
|-
 
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 19 kDa, 6.77  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 41 kDa, 5.369  
 
|-
 
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 489 bp, 163 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1128 bp, 376 aa  
 
|-
 
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yhdL]]'', ''[[yhdN]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ssuC]]'', ''[[ygaN]]''
 
|-
 
|-
|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" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB12714&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
|colspan="2" | '''Genetic context''' <br/> [[Image:sigM_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:ssuD_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 41: Line 41:
 
=== Database entries ===
 
=== Database entries ===
  
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/sigM-yhdLK.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ssuBACD-ygaN.html]
  
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13019]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10658]
  
 
=== Additional information===
 
=== Additional information===
Line 57: Line 57:
  
 
* '''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 ===
Line 84: Line 80:
 
* '''Swiss prot entry:'''
 
* '''Swiss prot entry:'''
  
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU09520]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU08860]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
Line 92: Line 88:
 
=Expression and regulation=
 
=Expression and regulation=
  
* '''Operon:''' ''[[sigM]]-[[yhdL]]-[[yhdK]]''
+
* '''Operon:''' ''[[ssuB]]-[[ssuA]]-[[ssuC]]-[[ssuD]]-[[ygaN]]''
  
* '''[[Sigma factor]]:''' [[SigM]]
+
* '''[[Sigma factor]]:''' [[SigA]]
  
 
* '''Regulation:'''  
 
* '''Regulation:'''  
Line 117: Line 113:
  
 
=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=
Line 123: Line 118:
 
=References=
 
=References=
  
 +
# van der Ploeg JR, Cummings NJ, Leisinger T, Connerton IF. (1998) Bacillus subtilis genes for the utilization of sulfur from aliphatic sulfonates. ''Microbiology'' '''Sep;144(Pt9):''' 2555-61.  [http://www.ncbi.nlm.nih.gov/sites/entrez/9782504 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 15:30, 25 April 2009

  • Description: aliphatic sulfonate monooxygenase

Gene name ssuD
Synonyms ygcA, yzeC
Essential no
Product aliphatic sulfonate monooxygenase
Function sulfonate reduction
MW, pI 41 kDa, 5.369
Gene length, protein length 1128 bp, 376 aa
Immediate neighbours ssuC, ygaN
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
SsuD 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):

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

Your additional remarks

References

  1. van der Ploeg JR, Cummings NJ, Leisinger T, Connerton IF. (1998) Bacillus subtilis genes for the utilization of sulfur from aliphatic sulfonates. Microbiology Sep;144(Pt9): 2555-61. PubMed
  2. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed