Difference between revisions of "Sandbox"

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−
* '''Description:''' xylose isomerase <br/><br/>
+
* '''Description:''' xylulokinase <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'''
−
|''xylA''
+
|''xylB''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yncA ''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || xylose isomerase
+
|style="background:#ABCDEF;" align="center"| '''Product''' || xylulokinase
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"|'''Function''' || utilization of xylan and xylose
 
|style="background:#ABCDEF;" align="center"|'''Function''' || utilization of xylan and xylose
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 50 kDa, 5.635  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 55 kDa, 6.459  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1335 bp, 445 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1497 bp, 499 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[xylR]]'', ''[[xylB]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[xylA]]'', ''[[yncB]]''
 
|-
 
|-
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/xylA_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/xylB_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/xylA_protein.txt Protein sequence]'''
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/xylB_protein.txt Protein sequence]'''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;color:#FF0000" align="center" | '''Caution: The sequence for this gene in SubtiList contains errors
+
|colspan="2" | '''Genetic context''' <br/> [[Image:xylB_context.gif]]
−
|-
 
−
|colspan="2" | '''Genetic context''' <br/> [[Image:xylA_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 46: Line 44:
 
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/xylAB.html]
 
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/xylAB.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10806]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10807]
  
 
=== Additional information===
 
=== Additional information===
Line 83: Line 81:
 
* '''Swiss prot entry:'''
 
* '''Swiss prot entry:'''
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU17600]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU17610]
  
−
* '''E.C. number:''' 5.3.1.5
+
* '''E.C. number:'''
  
 
=== Additional information===
 
=== Additional information===
Line 124: Line 122:
  
 
# 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  
−
# Dahl, M. K., J. Degenkolb, and W. Hillen. 1994. Transcription of the xyl operon is controlled in Bacillus subtilis by tandem overlapping operators spaced by four base-pairs. J. Mol. Biol. 243:413-424. [http://www.ncbi.nlm.nih.gov/sites/entrez/7966270 PubMed]
 
−
# Jacob S, Allmansberger R, Gärtner D, Hillen W (1991) Catabolite repression of the operon for xylose utilization from Bacillus subtilis W23 is mediated at the level of transcription and depends on a cis site in the xylA reading frame. Mol Gen Genet 229: 189-196. [http://www.ncbi.nlm.nih.gov/sites/entrez/1921970 PubMed]
 
−
# Kraus A, Hueck C, Gärtner D, Hillen W (1994) Catabolite repression of the Bacillus subtilis xyl operon involves a cis element functional in the context of an unrelated sequence, and glucose exerts additional xylR-dependent repression. J Bacteriol 176: 1738-1745. [http://www.ncbi.nlm.nih.gov/sites/entrez/8132469 PubMed]
 
−
# Gärtner D, Geißendörfer M, Hillen W. 1988. Expression of the Bacillus subtilis xyl operon is repressed at the level of transcription and is induced by xylose. J. Bacteriol. 170:3102-3109. [http://www.ncbi.nlm.nih.gov/sites/entrez/2454911 PubMed]
 
−
# Gärtner D, Degenkolb J, Ripperger JAE, Allmansberger R, Hillen W. 1992. Regulation of the Bacillus subtilis W23 xylose utilization operon: interaction of Xyl repressor with xyl operator and the inducer xylose. Mol. Gen. Genet. 232:415-422 [http://www.ncbi.nlm.nih.gov/sites/entrez/1588910 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 00:48, 3 April 2009

  • Description: xylulokinase

Gene name xylB
Synonyms yncA
Essential no
Product xylulokinase
Function utilization of xylan and xylose
MW, pI 55 kDa, 6.459
Gene length, protein length 1497 bp, 499 aa
Immediate neighbours xylA, yncB
Gene sequence (+200bp) Protein sequence
Genetic context
XylB 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

  • Regulation: repressed by glucose (CcpA) , carbon catabolite repression (CcpA), induction by xylose (XylR)
  • Regulatory mechanism: CcpA: transcription repression, CcpA: transcription repression, XylR: transcription repression
  • Additional information:

Biological materials

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

Labs working on this gene/protein

Wolfgang Hillen, Erlangen University, Germany Homepage

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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