Difference between revisions of "Sandbox"

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−
* '''Description:''' Sigma subunit of the RNA polymerase, Sigma-54, Sigma L <br/><br/>
+
* '''Description:''' glucuronate isomerase (D-glucuronate, D-galacturonate) <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'''
−
|''sigL''
+
|''uxaC''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yjmA ''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
+
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || RNA polymerase sigma-54 factor (sigma-L)
+
|style="background:#ABCDEF;" align="center"| '''Product''' || glucuronate isomerase (D-glucuronate, D-galacturonate)
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || utilization of arginin, acetoin, and fructose, required for cold adaptation
+
|style="background:#ABCDEF;" align="center"|'''Function''' || hexuronate utilization  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 49,5 kDa, 7.79
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 54 kDa, 5.174 
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1308 bp, 436 amino acids
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1419 bp, 473 aa
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yvfG]]'', ''[[yvfH]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ndh]]'', ''[[yjmB]]''
 
|-
 
|-
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/sigL_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/uxaC_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/sigL_protein.txt Protein sequence]'''
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/uxaC_protein.txt Protein sequence]'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:sigL_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:uxaC_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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=== Basic information ===
 
=== Basic information ===
  
−
* '''Coordinates:''' 3511532 - 3512839
+
* '''Coordinates:'''
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
−
 
−
The mutant is cold-sensitive and unable to use arginine as a single carbon source. [http://www.ncbi.nlm.nih.gov/sites/entrez/16585774  PubMed]
 
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/sigL.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/uxaC-yjmBCD-uxuA-yjmF-exuTR-uxaBA.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10748]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13204]
  
 
=== Additional information===
 
=== Additional information===
 +
  
 
=The protein=
 
=The protein=
Line 54: Line 53:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:''' Binding to promoters of the -12, -24 type
+
* '''Catalyzed reaction/ biological activity:'''  
  
−
* '''Protein family:''' sigma-54 factor family
+
* '''Protein family:'''
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
−
 
−
=== Genes/ operons controlled by SigL ===
 
−
''[[acoA]]-[[acoB]]-[[acoC]]-[[acoL]]'', ''[[rocA]]-[[rocB]]-[[rocC]]'', ''[[rocD]]-[[rocE]]-[[rocF]]'', ''[[rocG]]'', ''[[levD]]-[[levE]]-[[levF]]-[[levG]]-[[sacC]]'', ''[[ptb]]-[[bcd]]-[[buk]]-[[lpdV]]-[[bkdAA]]-[[bkdAB]]-[[bkdB]]''
 
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
Line 67: Line 63:
 
* '''Kinetic information:'''
 
* '''Kinetic information:'''
  
−
* '''Domains:'''
+
* '''Domains:'''  
−
** DNA binding domain (H-T-H motif) (324–343)
 
−
** pron box domain (413–421)
 
−
** 3 x Compositional bias domain (6–21),(32–53),(112–136)
 
  
 
* '''Modification:'''
 
* '''Modification:'''
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* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
  
−
* '''Interactions:''' SigL-[[RpoB]]-[[RpoC]]
+
* '''Interactions:'''
  
 
* '''Localization:'''
 
* '''Localization:'''
Line 86: Line 79:
 
* '''Structure:'''
 
* '''Structure:'''
  
−
* '''Swiss prot entry:''' [http://www.expasy.ch/cgi-bin/sprot-search-ac?P24219]
+
* '''Swiss prot entry:'''
 +
 
 +
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU12300]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU34200]
+
* '''E.C. number:'''
  
 
=== Additional information===
 
=== Additional information===
Line 98: Line 93:
 
* '''Sigma factor:'''  
 
* '''Sigma factor:'''  
  
−
* '''Regulation:''' repressed by glucose ([[CcpA]]) , neg. regulated by [[CcpA]] [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+16166551 PubMed]
+
* '''Regulation:''' repressed by glucose ([[CcpA]])   
  
−
* '''Regulatory mechanism:''' [[CcpA]]: transcription repression,  transcriptional roadblock
+
* '''Regulatory mechanism:''' [[CcpA]]: transcription repression  
  
−
* '''Additional information:'''
+
* '''Additional information:'''  
  
 
=Biological materials =
 
=Biological materials =
  
−
* '''Mutant:''' GP146 (aphA3), available in [[Stülke]] lab
+
* '''Mutant:'''
  
 
* '''Expression vector:'''
 
* '''Expression vector:'''
−
+
       
 
* '''lacZ fusion:'''
 
* '''lacZ fusion:'''
  
 
* '''GFP fusion:'''
 
* '''GFP fusion:'''
 +
 +
* '''two-hybrid system:'''
  
 
* '''Antibody:'''
 
* '''Antibody:'''
  
 
=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
−
 
−
[[Michel Debarbouille]], Pasteur Institute, Paris, France [http://www.pasteur.fr/ip/easysite/go/03b-00000m-0ob/recherche/departements-scientifiques/microbiologie/unites-et-groupes/unite-de-biologie-des-bacteries-pathogenes-a-gram-positif/les-membres-de-l-equipe Homepage]
 
  
 
=Your additional remarks=
 
=Your additional remarks=
Line 125: Line 120:
  
 
# Blencke et al. (2003) Transcriptional profiling of gene expression in response to glucose in ''Bacillus subtilis'': regulation of the central metabolic pathways. ''Metab Eng.'' '''5:''' 133-149  
 
# Blencke et al. (2003) Transcriptional profiling of gene expression in response to glucose in ''Bacillus subtilis'': regulation of the central metabolic pathways. ''Metab Eng.'' '''5:''' 133-149  
−
# Ali, N. O., Bignon, J., Rapoport, G., and Débarbouillé, M. (2001) Regulation of the acetoin catabolic pathway is controlled by sigma L in Bacillus subtilis. J. Bacteriol. 183, 2497-2504. [http://www.ncbi.nlm.nih.gov/sites/entrez/11274109  PubMed]
+
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]
−
# Belitsky BR, Sonenshein AL (1998) Role and regulation of Bacillus subtilis glutamate dehydrogenase genes. J Bacteriol 180:6298-6305. [http://www.ncbi.nlm.nih.gov/sites/entrez/9829940  PubMed]
 
−
# Choi SK, Saier MH Jr: (2005) Regulation of sigL expression by the catabolite control protein CcpA involves a roadblock mechanism in Bacillus subtilis: potential connection between carbon and nitrogen metabolism. J Bacteriol , 187:6856-6861. [http://www.ncbi.nlm.nih.gov/sites/entrez/16166551  PubMed]
 
−
# Débarbouillé M, Martin-Verstraete I, Kunst F, Rapoport G: (1991) The Bacillus subtilis sigL gene encodes an equivalent of (Sigma)54 from Gram-negative bacteria. Proc Natl Acad Sci USA , 88:9092-9096. [http://www.ncbi.nlm.nih.gov/sites/entrez/1924373  PubMed]
 
−
# Martin-Verstraete I, Débarbouillé M, Klier A, Rapoport G: (1992) Mutagenesis of the Bacillus subtilis ‘-12, -24’ promoter of the levanase operon and evidence for the existence of an upstream activating sequence. J Mol Biol , 226:85-99. [http://www.ncbi.nlm.nih.gov/sites/entrez/1619665  PubMed]
 
−
# Wiegeshoff et al.  (2006) Sigma L is important for cold shock adaptation of ''Bacillus subtilis''. J Bacteriol , 188: 3130-3133. [http://www.ncbi.nlm.nih.gov/sites/entrez/16585774  PubMed]
 

Revision as of 00:49, 3 April 2009

  • Description: glucuronate isomerase (D-glucuronate, D-galacturonate)

Gene name uxaC
Synonyms yjmA
Essential no
Product glucuronate isomerase (D-glucuronate, D-galacturonate)
Function hexuronate utilization
MW, pI 54 kDa, 5.174
Gene length, protein length 1419 bp, 473 aa
Immediate neighbours ndh, yjmB
Gene sequence (+200bp) Protein sequence
Genetic context
UxaC 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:
  • Interactions:
  • Localization:

Database entries

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

Additional information

Expression and regulation

  • Operon:
  • Sigma factor:
  • Regulation: repressed by glucose (CcpA)
  • Regulatory mechanism: CcpA: transcription repression
  • 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. Blencke et al. (2003) Transcriptional profiling of gene expression in response to glucose in Bacillus subtilis: regulation of the central metabolic pathways. Metab Eng. 5: 133-149
  2. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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