Difference between revisions of "Sandbox"

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−
* '''Description:''' co-[[sigma factor]] (with [[YvrI]]) <br/><br/>
+
* '''Description:''' RNA polymerase [[sigma factor]] YvrI <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'''
−
|''yvrHa''
+
|''yvrI''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' rsoA''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' sigO''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Essential''' || write here
+
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || co-[[sigma factor]] (with [[YvrI]])
+
|style="background:#ABCDEF;" align="center"| '''Product''' || co-[[sigma factor]] with [[YvrHa]]
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"|'''Function''' || RNA polymerase [[sigma factor]]
 
|style="background:#ABCDEF;" align="center"|'''Function''' || RNA polymerase [[sigma factor]]
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || xx,x kDa, y.yy
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 22 kDa, 9.779 
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || aaa bp, bbb amino acids
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 573 bp, 191 aa
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yvrI]]'', ''[[yvrHb]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yvrHa]]'', ''[[yvrJ]]''
 
|-
 
|-
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/genE_nucleotide.txt    Gene sequence      (+200bp)  ]'''
+
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB15313&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/genE_protein.txt Protein sequence]'''
 
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:YvrHa_yvrHb_context.GIF]]
+
|-
 +
|-
 +
|colspan="2" | '''Genetic context''' <br/> [[Image:yvrI_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 35: Line 37:
 
=== Basic information ===
 
=== Basic information ===
  
−
* '''Coordinates (CDS):'''
+
* '''Coordinates:'''
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
Line 41: Line 43:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' no entry
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yvrI-yvrHa.html]
  
−
* '''SubtiList entry:''' does not exist
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG14147]
  
 
=== Additional information===
 
=== Additional information===
  
−
The sequence of the former ''yvrH'' gene was corrected, and does now contain two genes, ''[[yvrHa]]'' and ''[[yvrHb]]''.
 
  
 
=The protein=
 
=The protein=
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* '''Swiss prot entry:'''
 
* '''Swiss prot entry:'''
  
−
* '''KEGG entry:''' no entry
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU33230]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
Line 120: Line 121:
 
=References=
 
=References=
  
−
# MacLellan et al. (2009) The YvrI alternative sigma factor is essential for acid stress induction of oxalate decarboxylase in ''Bacillus subtilis''. ''J. Bacteriol.'' '''191:''' 931-939. [http://www.ncbi.nlm.nih.gov/sites/entrez/19047353 PubMed]
+
# MacLellan et al. (2009) The YvrI alternative [[sigma factor]] is essential for acid stress induction of oxalate decarboxylase in ''Bacillus subtilis''. ''J. Bacteriol.'' '''191:''' 931-939. [http://www.ncbi.nlm.nih.gov/sites/entrez/19047353 PubMed]
 +
# Serizawa M, Kodama K, Yamamoto H, Kobayashi K, Ogasawara N, Sekiguchi J. (2005) Functional analysis of the YvrGHb two-component system of ''Bacillus subtilis'': identification of the regulated genes by DNA microarray and northern blot analyses. ''Biosci. Biotechnol. Biochem.'' '''69:''' 2155-2169. [http://www.ncbi.nlm.nih.gov/sites/entrez/16306698 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 23:20, 27 April 2009

Gene name yvrI
Synonyms sigO
Essential no
Product co-sigma factor with YvrHa
Function RNA polymerase sigma factor
MW, pI 22 kDa, 9.779
Gene length, protein length 573 bp, 191 aa
Immediate neighbours yvrHa, yvrJ
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
YvrI 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:
  • Localization:

Database entries

  • Structure:
  • Swiss prot entry:
  • KEGG entry: [3]
  • E.C. number:

Additional information

Expression and regulation

  • Regulation: induced by acidic growth conditions PubMed
  • 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. MacLellan et al. (2009) The YvrI alternative sigma factor is essential for acid stress induction of oxalate decarboxylase in Bacillus subtilis. J. Bacteriol. 191: 931-939. PubMed
  2. Serizawa M, Kodama K, Yamamoto H, Kobayashi K, Ogasawara N, Sekiguchi J. (2005) Functional analysis of the YvrGHb two-component system of Bacillus subtilis: identification of the regulated genes by DNA microarray and northern blot analyses. Biosci. Biotechnol. Biochem. 69: 2155-2169. PubMed
  3. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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