Difference between revisions of "Sandbox"

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* '''Description:''' B subunit of DNA gyrase<br/><br/>
+
* '''Description:''' write here <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'''
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|''gyrB''
+
|''gyrA''
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''novA ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''nalA ''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes   
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes   
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"| '''Product''' || DNA gyrase (subunit B) (EC 5.99.1.3)
+
|style="background:#ABCDEF;" align="center"| '''Product''' || DNA gyrase (subunit A) (EC 5.99.1.3)
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"|'''Function''' || initation of replication cycle and DNA elongation
 
|style="background:#ABCDEF;" align="center"|'''Function''' || initation of replication cycle and DNA elongation
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 71 kDa, 5.378  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 91 kDa, 5.215  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1914 bp, 638 aa  
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|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 2463 bp, 821 aa  
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' ||  
 
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' ||  
 
|-
 
|-
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|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/gyrB_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
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|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/gyrA_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
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|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/gyrB_protein.txt Protein sequence]'''
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/gyrA_protein.txt Protein sequence]'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:gyrB_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:gyrA_context.gif]]
 
|-
 
|-
 
|}
 
|}
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=== Database entries ===
 
=== Database entries ===
  
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* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yaaA-recF-yaaB-gyrB.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/gyrA.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10070]
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* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10071]
  
 
=== Additional information===
 
=== Additional information===
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* '''Protein family:'''
 
* '''Protein family:'''
  
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* '''Paralogous protein(s):''' [[GrlB]]
+
* '''Paralogous protein(s):''' [[GrlA]]
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
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* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
  
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* '''Interactions:''' [[GyrA]]-GyrB
+
* '''Interactions:''' GyrA-[[GyrB]]
  
 
* '''Localization:''' nucleoid-associated in actively growing cells [http://www.ncbi.nlm.nih.gov/sites/entrez/9539793 PubMed]
 
* '''Localization:''' nucleoid-associated in actively growing cells [http://www.ncbi.nlm.nih.gov/sites/entrez/9539793 PubMed]
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=Expression and regulation=
 
=Expression and regulation=
  
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* '''Operon:''' ''[[yaaA]]-[[recF]]-[[yaaB]]-[[gyrB]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/2987848 PubMed]
+
* '''Operon:''' ''gyrA'' [http://www.ncbi.nlm.nih.gov/sites/entrez/2987848 PubMed]
  
 
* '''Sigma factor:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/2987848 PubMed]
 
* '''Sigma factor:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/2987848 PubMed]
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* '''Regulatory mechanism:'''  
 
* '''Regulatory mechanism:'''  
  
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* '''Additional information:''' GyrB is subject to Clp-dependent proteolysis upon glucose starvation [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+17981983 PubMed]
+
* '''Additional information:''' GyrA is subject to Clp-dependent proteolysis upon glucose starvation [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+17981983 PubMed]
  
 
=Biological materials =
 
=Biological materials =

Revision as of 12:48, 9 February 2009

  • Description: write here

Gene name gyrA
Synonyms nalA
Essential yes
Product DNA gyrase (subunit A) (EC 5.99.1.3)
Function initation of replication cycle and DNA elongation
MW, pI 91 kDa, 5.215
Gene length, protein length 2463 bp, 821 aa
Immediate neighbours
Gene sequence (+200bp) Protein sequence
Genetic context
GyrA context.gif



The gene

Basic information

  • Coordinates:

Phenotypes of a mutant

essential

essential 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): GrlA

Extended information on the protein

  • Kinetic information:
  • Domains:
  • Modification:
  • Cofactor(s):
  • Effectors of protein activity:
  • Interactions: GyrA-GyrB
  • Localization: nucleoid-associated in actively growing cells PubMed

Database entries

  • Structure:
  • Swiss prot entry:
  • KEGG entry:
  • E.C. number:

Additional information

Expression and regulation

  • Regulation:
  • Regulatory mechanism:
  • Additional information: GyrA is subject to Clp-dependent proteolysis upon glucose starvation PubMed

Biological materials

  • Mutant:
  • Expression vector:
  • lacZ fusion:
  • GFP fusion:
  • two-hybrid system:
  • Antibody:

Labs working on this gene/protein

Your additional remarks

References

  1. Huang et al. (1998) Bipolar localization of Bacillus subtilis topoisomerase IV, an enzyme required for chromosome segregation. Proc. Natl. Acad. Sci. USA 95: 4652-4657. PubMed
  2. Gerth et al. (2008) Clp-dependent proteolysis down-regulates central metabolic pathways in glucose-starved Bacillus subtilis. J Bacteriol 190:321-331 PubMed
  3. Ogasawara et al. (1985) Structure and function of the region of the replication origin of the Bacillus subtilis chromosome. IV. Transcription of the oriC region and expression of DNA gyrase genes and other open reading frames.Nucl. Acids Res. 11: 2267-2279. PubMed
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