Difference between revisions of "Sandbox"

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* '''Description:''' two-component response regulator <br/><br/>
+
* '''Description:''' similar to ABC transporter (amino acid permease) <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'''
−
|''yvrHb''
+
|''yvsH''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yvrH ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
+
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || two-component response regulator
+
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || regulation cell surface maintenance
+
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 26.6 kDa, 5.23
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 50 kDa, 9.743 
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 714 bp, 237 amino acids
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1407 bp, 469 aa
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yvrHa]]'', ''[[yvrG]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[fhuD]]'', ''[[sspJ]]''
 
|-
 
|-
−
|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:CAB15339&#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:yvsH_context.gif]]
 +
<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
 
|-
 
|-
 
|}
 
|}
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=== Basic information ===
 
=== Basic information ===
  
−
* '''Locus tag:'''
+
* '''Locus tag:''' BSU33330
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
−
 
−
unusual autolysis and higher susceptibility to cell envelope antibiotics (bacitracin, aztreonam, cefepime, fosfomycin)  [http://www.ncbi.nlm.nih.gov/sites/entrez/16306698 PubMed]
 
  
 
=== Database entries ===
 
=== Database entries ===
Line 45: Line 43:
 
* '''DBTBS entry:''' no entry
 
* '''DBTBS entry:''' no entry
  
−
* '''SubtiList entry:''' no entry
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG14154]
  
 
=== Additional information===
 
=== Additional information===
 +
  
 
=The protein=
 
=The protein=
Line 53: Line 52:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:''' transcription activator  [http://www.ncbi.nlm.nih.gov/sites/entrez/16306698 PubMed]
+
* '''Catalyzed reaction/ biological activity:'''  
−
 
 
−
* '''Protein family:''' OmpR family
 
−
 
 
−
* '''Paralogous protein(s):'''
 
−
 
 
−
=== The YvrHb regulon ===
 
  
−
subject to positive control: ''[[dltA]]-[[dltB]]-[[dltC]]-[[dltD]]-[[dltE]], [[sigX]]-[[rsiX]], [[sunA]], [[sunT]]-[[bdbA]]-[[yolJ]]-[[bdbB]], [[wapA]]-[[yxxG]], [[wprA]], [[yvrI]]-[[yvrHa]]''  [http://www.ncbi.nlm.nih.gov/sites/entrez/16306698 PubMed]
+
* '''Protein family:''' amino acid-polyamine-organocation (APC) superfamily (according to Swiss-Prot)
  
−
subject to negative control: ''[[lytA]]-[[lytB]]-[[lytC]]''  [http://www.ncbi.nlm.nih.gov/sites/entrez/16306698 PubMed]
+
* '''Paralogous protein(s):'''
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
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* '''Kinetic information:'''
 
* '''Kinetic information:'''
  
−
* '''Domains:'''
+
* '''Domains:'''  
  
−
* '''Modification:''' phosphorylation (Asp) by [[YvrG]]  [http://www.ncbi.nlm.nih.gov/sites/entrez/16306698 PubMed]
+
* '''Modification:'''
  
 
* '''Cofactor(s):'''
 
* '''Cofactor(s):'''
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* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
  
−
* '''Interactions:''' YvrG-[[YvrHb]]  [http://www.ncbi.nlm.nih.gov/sites/entrez/16306698 PubMed]
+
* '''Interactions:'''
  
−
* '''Localization:''' cytoplasm (according to Swiss-Prot)
+
* '''Localization:''' cell membrane (according to Swiss-Prot),  membrane [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]
  
 
=== Database entries ===
 
=== Database entries ===
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* '''Structure:'''
 
* '''Structure:'''
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P94504 P94504]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/O32204 O32204]
  
−
* '''KEGG entry:''' no entry
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU33330]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
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* '''Regulatory mechanism:'''  
 
* '''Regulatory mechanism:'''  
  
−
* '''Additional information:'''
+
* '''Additional information:'''  
  
 
=Biological materials =
 
=Biological materials =
Line 125: Line 118:
 
=References=
 
=References=
  
−
<pubmed>16306698, </pubmed>
+
<pubmed>18763711, </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]
+
# 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]
 
# 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 13:52, 8 June 2009

  • Description: similar to ABC transporter (amino acid permease)

Gene name yvsH
Synonyms
Essential no
Product unknown
Function unknown
MW, pI 50 kDa, 9.743
Gene length, protein length 1407 bp, 469 aa
Immediate neighbours fhuD, sspJ
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
YvsH context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Locus tag: BSU33330

Phenotypes of a mutant

Database entries

  • DBTBS entry: no entry
  • SubtiList entry: [1]

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity:
  • Protein family: amino acid-polyamine-organocation (APC) superfamily (according to Swiss-Prot)
  • Paralogous protein(s):

Extended information on the protein

  • Kinetic information:
  • Domains:
  • Modification:
  • Cofactor(s):
  • Effectors of protein activity:
  • Interactions:
  • Localization: cell membrane (according to Swiss-Prot), membrane PubMed

Database entries

  • Structure:
  • KEGG entry: [2]
  • E.C. number:

Additional information

Expression and regulation

  • Operon:
  • 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

Hannes Hahne, Susanne Wolff, Michael Hecker, Dörte Becher
From complementarity to comprehensiveness--targeting the membrane proteome of growing Bacillus subtilis by divergent approaches.
Proteomics: 2008, 8(19);4123-36
[PubMed:18763711] [WorldCat.org] [DOI] (I p)

  1. Hahne et al. (2008) From complementarity to comprehensiveness - targeting the membrane proteome of growing Bacillus subtilis by divergent approaches. Proteomics 8: 4123-4136 PubMed
  2. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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