Difference between revisions of "Sandbox"

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−
* '''Description:''' tRNA-Ala
+
* '''Description:''' xylose isomerase <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'''
−
|''trnI-Ala''
+
|''xylA''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''trnH ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || transfer RNA-Ala
+
|style="background:#ABCDEF;" align="center"| '''Product''' || xylose isomerase
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || translation
+
|style="background:#ABCDEF;" align="center"|'''Function''' || utilization of xylan and xylose
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length''' || 76 bp
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 50 kDa, 5.635 
−
|-|-
 
−
 
 
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[trnI-Pro]]'', ''[[rrnH-16S]]''
 
 
|-
 
|-
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/trnI-Ala_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1335 bp, 445 aa
−
|style="background:#FAF8CC;" align="center"|'''  '''
 
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:trnI-Ala_context.gif]]
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[xylR]]'', ''[[xylB]]''
 +
|-
 +
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB13644&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 +
|-
 +
|-
 +
|-
 +
|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 31: Line 33:
 
<br/><br/>
 
<br/><br/>
  
−
<br/><br/><br/><br/><br/>
 
 
=The gene=
 
=The gene=
  
Line 42: Line 43:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' no entry
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/xylAB.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG00043]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10806]
−
 
−
* '''Structure:'''
 
  
 
=== Additional information===
 
=== 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:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU17600]
 +
 
 +
* '''E.C. number:''' 5.3.1.5
 +
 
 +
=== Additional information===
  
 
=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:'''  
+
* '''Operon:''' ''[[xylA]]-[[xylB]]''
  
−
* '''Sigma factor:'''  
+
* '''[[Sigma factor]]:''' [[SigA]]
  
−
* '''Regulation:'''  
+
* '''Regulation:''' repressed by glucose ([[CcpA]]) ,  carbon catabolite repression ([[CcpA]]), induction by xylose ([[XylR]])
  
−
* '''Regulatory mechanism:'''  
+
* '''Regulatory mechanism:''' [[CcpA]]: transcription repression,  [[CcpA]]: transcription repression, [[XylR]]: transcription repression
  
−
* '''Additional information:'''  
+
* '''Additional information:'''
  
 
=Biological materials =
 
=Biological materials =
Line 80: Line 115:
  
 
=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
 +
 +
[[Wolfgang Hillen]], Erlangen University, Germany [http://www.biologie.uni-erlangen.de/mibi/index2.html Homepage]
  
 
=Your additional remarks=
 
=Your additional remarks=
Line 85: Line 122:
 
=References=
 
=References=
  
 +
 +
# 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 16:46, 25 April 2009

  • Description: xylose isomerase

Gene name xylA
Synonyms
Essential no
Product xylose isomerase
Function utilization of xylan and xylose
MW, pI 50 kDa, 5.635
Gene length, protein length 1335 bp, 445 aa
Immediate neighbours xylR, xylB
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
XylA 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: 5.3.1.5

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. 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. PubMed
  2. 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. PubMed
  3. 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. PubMed
  4. 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. PubMed
  5. 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 PubMed
  6. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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