Difference between revisions of "Sandbox"

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* '''Description:''' write here <br/><br/>
+
* '''Description:''' co-[[sigma factor]] (with [[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'''
−
|''paiA''
+
|''yvrHa''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' rsoA''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
+
|style="background:#ABCDEF;" align="center"| '''Essential''' || write here
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || transcriptional regulator
+
|style="background:#ABCDEF;" align="center"| '''Product''' || co-[[sigma factor]] (with [[YvrI]])
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || negative regulation of sporulation, septation and <br/>degradative enzyme genes (aprE, nprE, phoA, sacB)
+
|style="background:#ABCDEF;" align="center"|'''Function''' || RNA polymerase [[sigma factor]]
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 19 kDa, 5.018 
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || xx,x kDa, y.yy
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 516 bp, 172 aa
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || aaa bp, bbb amino acids
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[paiB]]'', ''[[yutM]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yvrI]]'', ''[[yvrHb]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB15205&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/genE_nucleotide.txt    Gene sequence      (+200bp)  ]'''
 +
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/genE_protein.txt Protein sequence]'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:paiA_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:YvrHa_yvrHb_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/>
  
 
=The gene=
 
=The gene=
Line 35: Line 35:
 
=== Basic information ===
 
=== Basic information ===
  
−
* '''Coordinates:'''
+
* '''Coordinates (CDS):'''
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
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* '''DBTBS entry:''' no entry
 
* '''DBTBS entry:''' no entry
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10695]
+
* '''SubtiList entry:''' does not exist
  
 
=== 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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* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
  
−
* '''Interactions:''' [[AprE]]-[[PaiA]],  
+
* '''Interactions:''' [[YvrI]]-[[YvrHa]], [[YvrI]]-[[YvrHa]] [http://www.ncbi.nlm.nih.gov/sites/entrez/19047353 PubMed]
  
 
* '''Localization:'''
 
* '''Localization:'''
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* '''Swiss prot entry:'''
 
* '''Swiss prot entry:'''
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU32150]
+
* '''KEGG entry:''' no entry
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
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=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:'''  
+
* '''Operon:''' ''[[yvrI]]-[[yvrHa]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/19047353 PubMed]
  
−
* '''[[Sigma factor]]:'''  
+
* '''[[Sigma factor]]:''' [[YvrI]]-[[YvrHa]] [http://www.ncbi.nlm.nih.gov/sites/entrez/19047353 PubMed]
  
−
* '''Regulation:'''  
+
* '''Regulation:''' induced by acidic growth conditions [http://www.ncbi.nlm.nih.gov/sites/entrez/19047353 PubMed]
  
−
* '''Regulatory mechanism:'''  
+
* '''Regulatory mechanism:''' activated by [[YvrHb]]  [http://www.ncbi.nlm.nih.gov/sites/entrez/16306698 PubMed]
  
−
* '''Additional information:'''  
+
* '''Additional information:'''
  
 
=Biological materials =
 
=Biological materials =
Line 113: Line 114:
  
 
=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=
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=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]
 
# 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 00:20, 28 April 2009

Gene name yvrHa
Synonyms rsoA
Essential write here
Product co-sigma factor (with YvrI)
Function RNA polymerase sigma factor
MW, pI xx,x kDa, y.yy
Gene length, protein length aaa bp, bbb amino acids
Immediate neighbours yvrI, yvrHb
Gene sequence (+200bp) Protein sequence
Genetic context
YvrHa yvrHb context.GIF



The gene

Basic information

  • Coordinates (CDS):

Phenotypes of a mutant

Database entries

  • DBTBS entry: no entry
  • SubtiList entry: does not exist

Additional information

The sequence of the former yvrH gene was corrected, and does now contain two genes, yvrHa and yvrHb.

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: no entry
  • 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. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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