Difference between revisions of "Sandbox"

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* '''Description:''' succinate dehydrogenase(cytochrome b558 subunit) <br/><br/>
+
* '''Description:''' flagellin protein <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'''
−
|''sdhC''
+
|''hag''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
 
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
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|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || succinate dehydrogenase (cytochrome b558 subunit)
+
|style="background:#ABCDEF;" align="center"| '''Product''' || flagellin protein
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || TCA cycle
+
|style="background:#ABCDEF;" align="center"|'''Function''' || movement and chemotaxis
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 22 kDa, 9.831  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 32 kDa, 4.782  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 606 bp, 202 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 912 bp, 304 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yslB]], [[sdhA]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yvyC]]'', ''[[csrA]]''
 
|-
 
|-
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/sdhC_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/hag_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/sdhC_protein.txt Protein sequence]'''
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/hag_protein.txt Protein sequence]'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:sdhC_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:hag_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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===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
 +
 +
No swarming motility on B medium. [http://www.ncbi.nlm.nih.gov/sites/entrez/19202088 PubMed]
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/sdhCAB.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/hag.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10351]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10655]
  
 
=== Additional information===
 
=== Additional information===
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* '''Protein family:'''
 
* '''Protein family:'''
  
−
* '''Paralogous protein(s):'''
+
* '''Paralogous protein(s):''' [[YvzB]] (C-terminal domain of Hag)
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
Line 73: Line 75:
 
* '''Interactions:'''
 
* '''Interactions:'''
  
−
* '''Localization:''' membrane [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed] ,  membrane protein [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]
+
* '''Localization:''' membrane [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]  
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1NEK 1NEK] (''E. coli'')
+
* '''Structure:'''
  
 
* '''Swiss prot entry:'''
 
* '''Swiss prot entry:'''
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU28450]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU35360]
  
−
* '''E.C. number:''' 1.3.99.1
+
* '''E.C. number:'''
  
 
=== Additional information===
 
=== Additional information===
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=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''[[sdhC]]''-''[[sdhA]]''-''[[sdhB]]''
+
* '''Operon:''' ''[[hag]]''
−
 
 
−
* '''Sigma factor:''' [[SigA]]
 
  
−
* '''Regulation:''' constitutive
+
* '''Sigma factor:''' [[SigD]]
  
−
* '''Regulatory mechanism:''' [[FsrA]]: translational repression [http://www.ncbi.nlm.nih.gov/pubmed/18697947 PubMed]
+
* '''Regulation:'''  
  
 +
* '''Regulatory mechanism:'''
  
 
* '''Additional information:'''
 
* '''Additional information:'''
Line 102: Line 103:
 
=Biological materials =
 
=Biological materials =
  
−
* '''Mutant:''' GP743 (''sdhCA'', cat), available in [[Stülke]] lab
+
* '''Mutant:'''
  
 
* '''Expression vector:'''
 
* '''Expression vector:'''
Line 120: Line 121:
 
=References=
 
=References=
  
−
# 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]# 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]
+
# 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]
−
# Gaballa A, Antelmann H, Aguilar C, Khakh SK, Song KB, Smaldone GT, Helmann JD (2008) The Bacillus subtilis iron-sparing response is mediated by a Fur-regulated small RNA and three small, basic proteins. PNAS 105: 11927-11932. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]
+
# Hamze et al. (2009) Identification of genes required for different stages of dendritic swarming in ''Bacillus subtilis'', with a novel role for ''phrC''. ''Microbiology'' '''155:''' 398-412. [http://www.ncbi.nlm.nih.gov/sites/entrez/19202088 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 15:17, 25 March 2009

  • Description: flagellin protein

Gene name hag
Synonyms
Essential no
Product flagellin protein
Function movement and chemotaxis
MW, pI 32 kDa, 4.782
Gene length, protein length 912 bp, 304 aa
Immediate neighbours yvyC, csrA
Gene sequence (+200bp) Protein sequence
Genetic context
Hag context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Coordinates:

Phenotypes of a mutant

No swarming motility on B medium. PubMed

Database entries

  • DBTBS entry: [1]
  • SubtiList entry: [2]

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity:
  • Protein family:
  • Paralogous protein(s): YvzB (C-terminal domain of Hag)

Extended information on the protein

  • Kinetic information:
  • Domains:
  • Modification:
  • Cofactor(s):
  • Effectors of protein activity:
  • Interactions:
  • Localization: membrane PubMed

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. 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. Hamze et al. (2009) Identification of genes required for different stages of dendritic swarming in Bacillus subtilis, with a novel role for phrC. Microbiology 155: 398-412. PubMed
  3. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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