Difference between revisions of "Sandbox"

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* '''Description:''' RNA polymerase [[sigma factor]] SigB <br/><br/>
+
* '''Description:''' probable pantothenate kinase <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'''
−
|''sigB''
+
|''coaA''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''rpoF ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yqjS ''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || RNA polymerase [[sigma factor]] SigB
+
|style="background:#ABCDEF;" align="center"| '''Product''' || probable pantothenate kinase
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || general stress response
+
|style="background:#ABCDEF;" align="center"|'''Function''' || biosynthesis of coenzyme A
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: <br/>[http://subtiwiki.uni-goettingen.de/pathways/stress_response.html Stress]'''
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 36 kDa, 5.894 
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 29 kDa, 5.418 
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 957 bp, 319 aa
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 792 bp, 264 aa
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yqjT]]'', ''[[dsdA]]''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[rsbW]]'', ''[[rsbX]]''
+
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB14308&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB12280&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
+
|colspan="2" | '''Genetic context''' <br/> [[Image:coaA_context.gif]]
−
|-
 
−
|colspan="2" | '''Genetic context''' <br/> [[Image:sigB_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 ===
  
−
* '''Locus tag:''' BSU04730
+
* '''Locus tag:''' BSU23760
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
Line 43: Line 41:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/rsbRSTUVW-sigB-rsbX.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yqjPQ-dsdA-coaA-yqjT.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10735]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11748]
  
 
=== Additional information===
 
=== Additional information===
Line 54: Line 52:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:'''  
+
* '''Catalyzed reaction/ biological activity:''' ATP + (R)-pantothenate = ADP + (R)-4'-phosphopantothenate (according to Swiss-Prot)
  
−
* '''Protein family:''' SigB subfamily (according to Swiss-Prot)
+
* '''Protein family:''' prokaryotic pantothenate kinase family (according to Swiss-Prot)
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
−
 
−
=== Genes/ operons controlled by SigB ===
 
−
 
−
''[[csbB]]'', ''[[ctc]]'', ''[[gsiB]]'', ''[[katE]], [[lexA]],[[licR]], [[sfA]], [[xpf]], [[yaaH]], [[ydeC]], [[ytzE]], [[yvaN]], [[ywhH]]'',
 
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
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* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
  
−
* '''Interactions:''' [[SigB]]-[[RsbW]]
+
* '''Interactions:'''
  
 
* '''Localization:'''
 
* '''Localization:'''
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* '''Structure:'''
 
* '''Structure:'''
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P06574 P06574]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P54556 P54556]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU04730]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU23760]
  
−
* '''E.C. number:'''
+
* '''E.C. number:''' [http://www.expasy.org/enzyme/2.7.1.33 2.7.1.33]
  
 
=== Additional information===
 
=== Additional information===
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=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:'''  
+
* '''Operon:''' ''[[yqjP]]-[[yqjQ]]-[[dsdA]]-[[coaA]]-[[yqjT]]''
−
** ''[[rsbR]]-[[rsbS]]-[[rsbT]]-[[rsbU]]-[[rsbV]]-[[rsbW]]-[[sigB]]-[[rsbX]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/8002610 PubMed]
+
 
−
** ''[[rsbV]]-[[rsbW]]-[[sigB]]-[[rsbX]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/2170324 PubMed]
 
−
 
 
* '''[[Sigma factor]]:'''  
 
* '''[[Sigma factor]]:'''  
−
** ''[[rsbR]]'': [[SigA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/8002610 PubMed]
 
−
** ''[[rsbV]]:'' [[SigB]] [http://www.ncbi.nlm.nih.gov/pubmed/11544224 PubMed]
 
  
−
* '''Regulation:'''
+
* '''Regulation:'''  
−
** ''[[rsbV]]:'' induced by stress ([[SigB]]) [http://www.ncbi.nlm.nih.gov/pubmed/11544224 PubMed]
+
 
 +
* '''Regulatory mechanism:'''
  
 
* '''Additional information:'''
 
* '''Additional information:'''
Line 122: Line 113:
  
 
=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
−
 
−
* [[Bill Haldenwang]], San Antonio, USA
 
−
* [[Chet Price]], Davis, USA [http://foodscience.ucdavis.edu/price_lab/pricelab.html homepage]
 
  
 
=Your additional remarks=
 
=Your additional remarks=
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=References=
 
=References=
  
−
<pubmed>8655572,18035607,3123466,8682769,11717291,8460143,10369900,3112122,8468294,8458834,13129942,6784117,12867438,3100810,8253681,12270815,12486038,8764398,3027048,7601843,15342585,17575448,15342582,10482513,8002610,11591687,10220166,17586624,9767581,3016731,11902719,14651641,10503549,15205443,6405278,10383961,15312768,17498739,11377871,15805528 10482513 11544224 11532142 6790515 116131, </pubmed>
+
<pubmed>1328157,, </pubmed>
−
# H&ouml;per et al. (2005) Comprehensive Characterization of the Contribution of Individual [[SigB]]-Dependent General Stress Genes to Stress Resistance of ''Bacillus subtilis''. J. Bact. '''187:''' 2810-2826  [http://www.ncbi.nlm.nih.gov/pubmed/15805528 PubMed]
 
−
# Petersohn, A., Bernhardt, J., Gerth, U., Höper, D., Koburger, T., Völker, U. and Hecker, M. 1999. Identification of sigma(B)-dependent genes in Bacillus subtilis using a promoter consensus-directed search and oligonucleotide hybridization. J. Bacteriol. 181: 5718-5724. [http://www.ncbi.nlm.nih.gov/sites/entrez/10482513 PubMed]
 
−
# Petersohn, A., Brigulla, M., Haas, S., Hoheisel, J. D., Völker, U. and Hecker, M. 2001. Global analysis of the general stress reponse of Bacillus subtilis. J. Bacteriol. 183: 5617-5631. [http://www.ncbi.nlm.nih.gov/sites/entrez/11544224 PubMed]
 
−
# Price, C. W., Fawcett, P., Cérémonie, H., Su, N., Murphy, C. K. and Youngman, P. 2001. Genome-wide analysis of the general stress response in Bacillus subtilis. Mol. Microbiol. 41: 757-774. [http://www.ncbi.nlm.nih.gov/sites/entrez/11532142 PubMed]
 
−
# Ollington, J. F., Haldenwang, W. G., Huynh, T. V. and Losick, R. 1981. Developmentally regulated transcription in a cloned segment of the Bacillus subtilis chromosome. J. Bacteriol. 147: 432-442. [http://www.ncbi.nlm.nih.gov/sites/entrez/6790515 PubMed]
 
−
# Haldenwang, W. G. & Losick, R. (1979). A modified RNA polymerase transcribes a cloned gene under sporulation control in Bacillus subtilis. Nature 282, 256-260 [http://www.ncbi.nlm.nih.gov/pubmed/116131 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 15:50, 13 June 2009

  • Description: probable pantothenate kinase

Gene name coaA
Synonyms yqjS
Essential no
Product probable pantothenate kinase
Function biosynthesis of coenzyme A
MW, pI 36 kDa, 5.894
Gene length, protein length 957 bp, 319 aa
Immediate neighbours yqjT, dsdA
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
CoaA context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Locus tag: BSU23760

Phenotypes of a mutant

Database entries

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

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity: ATP + (R)-pantothenate = ADP + (R)-4'-phosphopantothenate (according to Swiss-Prot)
  • Protein family: prokaryotic pantothenate kinase family (according to Swiss-Prot)
  • Paralogous protein(s):

Extended information on the protein

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

Database entries

  • Structure:
  • KEGG entry: [3]

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. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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