Difference between revisions of "Sandbox"

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−
* '''Description:''' gluconokinase <br/><br/>
+
* '''Description:''' imidazoleglycerol-phosphate dehydratase <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'''
−
|''gntK''
+
|''hisB''
 
|-
 
|-
 
|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''' || gluconokinase
+
|style="background:#ABCDEF;" align="center"| '''Product''' || imidazoleglycerol-phosphate dehydratase
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || gluconate utilization
+
|style="background:#ABCDEF;" align="center"|'''Function''' || biosynthesis of histidine
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 56 kDa, 5.517  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 21 kDa, 5.598  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1539 bp, 513 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 582 bp, 194 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[gntR]]'', ''[[gntP]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[hisH]]'', ''[[hisD]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB16043&#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:CAB15495&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:gntK_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:hisB_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>
 
|-
 
|-
Line 35: Line 35:
 
=== Basic information ===
 
=== Basic information ===
  
−
* '''Locus tag:''' BSU40060
+
* '''Locus tag:''' BSU34900
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
Line 41: Line 41:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/gntRKPZ.html]
+
* '''DBTBS entry:''' no entry
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10649]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12598]
  
 
=== Additional information===
 
=== Additional information===
Line 52: Line 52:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:''' ATP + D-gluconate = ADP + 6-phospho-D-gluconate (according to Swiss-Prot)  
+
* '''Catalyzed reaction/ biological activity:''' D-erythro-1-(imidazol-4-yl)glycerol 3-phosphate = 3-(imidazol-4-yl)-2-oxopropyl phosphate + H<sub>2</sub>O (according to Swiss-Prot)  
  
−
* '''Protein family:''' FGGY kinase family (according to Swiss-Prot)
+
* '''Protein family:''' imidazoleglycerol-phosphate dehydratase family (according to Swiss-Prot)
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
Line 72: Line 72:
 
* '''Interactions:'''
 
* '''Interactions:'''
  
−
* '''Localization:'''
+
* '''Localization:''' cytoplasm (according to Swiss-Prot)
  
 
=== Database entries ===
 
=== Database entries ===
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* '''Structure:'''
 
* '''Structure:'''
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P12011 P12011]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/O34683 O34683]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU40060]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU34900]
  
−
* '''E.C. number:''' [http://www.expasy.org/enzyme/2.7.1.12 2.7.1.12]
+
* '''E.C. number:''' [http://www.expasy.org/enzyme/4.2.1.19 4.2.1.19]
  
 
=== Additional information===
 
=== Additional information===
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=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''[[gntR]]-[[gntK]]-[[gntP]]-[[gntZ]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/10746760 PubMed1][http://www.ncbi.nlm.nih.gov/sites/entrez/3020045 PubMed2]
+
* '''Operon:'''  
  
−
* '''[[Sigma factor]]:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/3020045 PubMed]
+
* '''[[Sigma factor]]:'''  
  
−
* '''Regulation:'''  
+
* '''Regulation:''' repressed by casamino acids [http://www.ncbi.nlm.nih.gov/pubmed/12107147 PubMed]
−
**  induced by gluconate ([[GntR]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/3020045 PubMed]
 
−
** repressed by glucose ([[CcpA]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/8370661 PubMed]
 
  
 
* '''Regulatory mechanism:'''  
 
* '''Regulatory mechanism:'''  
−
** [[GntR]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/3020045 PubMed]
 
−
** [[CcpA]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/10666464 PubMed]
 
  
−
* '''Additional information:'''
+
* '''Additional information:'''  
  
 
=Biological materials =
 
=Biological materials =
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=References=
 
=References=
  
−
 
+
# M&#228;der et al. (2002) Transcriptome and Proteome Analysis of ''Bacillus subtilis'' Gene Expression Modulated by Amino Acid Availability. ''J. Bacteriol'' '''184:''' 1844288-4295 [http://www.ncbi.nlm.nih.gov/pubmed/12107147 PubMed]
−
# Fujita Y, Fujita T, Miwa Y, Nihashi J, Aratani Y. (1986) Organization and transcription of the gluconate operon, gnt, of Bacillus subtilis. ''J Biol Chem.'' '''Oct 15;261(29):''' 13744-53. [http://www.ncbi.nlm.nih.gov/sites/entrez/3020045 PubMed]
 
−
# Reizer A., Deutscher J., Saier M.H. Jr., Reizer J. (1991) Analysis of the gluconate (gnt) operon of Bacillus subtilis. ''Mol. Microbiol.'' '''5:''' 1081-1089. [http://www.ncbi.nlm.nih.gov/sites/entrez/1659648 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 18:49, 7 June 2009

  • Description: imidazoleglycerol-phosphate dehydratase

Gene name hisB
Synonyms
Essential no
Product imidazoleglycerol-phosphate dehydratase
Function biosynthesis of histidine
MW, pI 21 kDa, 5.598
Gene length, protein length 582 bp, 194 aa
Immediate neighbours hisH, hisD
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
HisB context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Locus tag: BSU34900

Phenotypes of a mutant

Database entries

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

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity: D-erythro-1-(imidazol-4-yl)glycerol 3-phosphate = 3-(imidazol-4-yl)-2-oxopropyl phosphate + H2O (according to Swiss-Prot)
  • Protein family: imidazoleglycerol-phosphate dehydratase 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: cytoplasm (according to Swiss-Prot)

Database entries

  • Structure:
  • KEGG entry: [2]

Additional information

Expression and regulation

  • Operon:
  • Regulation: repressed by casamino acids PubMed
  • 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. Mäder et al. (2002) Transcriptome and Proteome Analysis of Bacillus subtilis Gene Expression Modulated by Amino Acid Availability. J. Bacteriol 184: 1844288-4295 PubMed
  2. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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