Difference between revisions of "Sandbox"

From SubtiWiki
Jump to: navigation, search
Line 1: Line 1:
−
* '''Description:''' transcriptional antiterminator for the sacP-sacA operon <br/><br/>
+
* '''Description:''' similar to nitrite transporter <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'''
−
|''sacT''
+
|''ywcJ''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ipa-47d ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ipa-48r ''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || transcriptional antiterminator
+
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || regulation of sucrose utilization
+
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 31 kDa, 5.587  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 28 kDa, 7.678  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 828 bp, 276 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 768 bp, 256 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ywcJ]]'', ''[[ywcI]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[sacP]]'', ''[[sacT]]''
 
|-
 
|-
 
|colspan="2" style="background:#FAF8CC;" align="center"|'''Hier soll was neues rein'''
 
|colspan="2" style="background:#FAF8CC;" align="center"|'''Hier soll was neues rein'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:sacT_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:ywcJ_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 41: Line 41:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/sacT.html]
+
* '''DBTBS entry:''' no entry
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10593]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10594]
  
 
=== Additional information===
 
=== Additional information===
Line 52: Line 52:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:''' binding to the mRNA of the ''[[sacP]]-[[sacA]]'' operon, causes transcription antitermination (in presence of sucrose and absence of glucose)
+
* '''Catalyzed reaction/ biological activity:'''  
  
−
* '''Protein family:''' BglG family of antiterminators
+
* '''Protein family:'''
  
−
* '''Paralogous protein(s):''' [[LicT]], [[SacY]], [[GlcT]]
+
* '''Paralogous protein(s):''' [[YrhG]]
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
Line 80: Line 80:
 
* '''Swiss prot entry:'''
 
* '''Swiss prot entry:'''
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU38070]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU38060]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
Line 92: Line 92:
 
* '''[[Sigma factor]]:'''  
 
* '''[[Sigma factor]]:'''  
  
−
* '''Regulation:''' repressed by casamino acids [http://www.ncbi.nlm.nih.gov/pubmed/12107147 PubMed]
+
* '''Regulation:''' induced under anaerobic conditions ([[Rex]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/16207915 PubMed]
  
−
* '''Regulatory mechanism:'''  
+
* '''Regulatory mechanism:''' [[Rex]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/16207915 PubMed]
  
−
* '''Additional information:'''  
+
* '''Additional information:'''
  
 
=Biological materials =
 
=Biological materials =
Line 118: Line 118:
 
=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]
 
−
# Débarbouillé, M., Arnaud, M., Fouet, A., Klier, A., and  Rapoport, G. (1990) The sacT gene regulating the ''sacPA'' operon in ''Bacillus subtilis'' shares strong homology with transcriptional antiterminators. J Bacteriol 172: 3966-3973. [http://www.ncbi.nlm.nih.gov/sites/entrez/2163394 PubMed]
 
−
# Arnaud, M., Vary, P., Zagorec, M., Klier, A., Débarbouillé, M., Postma, P., and Rapoport, G. (1992) Regulation of the ''sacPA'' operon of ''Bacillus subtilis'': identification of phosphotransferase system components involved in SacT activity. J Bacteriol 174: 3161-3170. [http://www.ncbi.nlm.nih.gov/sites/entrez/1577686 PubMed]
 
−
# Arnaud, M., Débarbouillé, M., Rapoport, G., Saier, M. H., and Reizer, J. (1996) In vitro reconstitution of transcriptional antitermination by the SacT and SacY proteins of ''Bacillus subtilis''. J Biol Chem 271: 18966-18972. [http://www.ncbi.nlm.nih.gov/sites/entrez/8702561 PubMed]
 
−
# Aymerich, S. and Steinmetz, M. (1992) Specificity determinants and structural features in the RNA target of the bacterial antiterminator proteins of the BglG/SacY family. Proc. Natl. Acad. Sci. USA 89, 10410-10414. [http://www.ncbi.nlm.nih.gov/sites/entrez/1279678 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 17:07, 15 April 2009

  • Description: similar to nitrite transporter

Gene name ywcJ
Synonyms ipa-48r
Essential no
Product unknown
Function unknown
MW, pI 28 kDa, 7.678
Gene length, protein length 768 bp, 256 aa
Immediate neighbours sacP, sacT
Hier soll was neues rein
Genetic context
YwcJ context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Coordinates:

Phenotypes of a mutant

Database entries

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

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity:
  • Protein family:
  • Paralogous protein(s): YrhG

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: [2]
  • E.C. number:

Additional information

Expression and regulation

  • Operon:
  • Regulation: induced under anaerobic conditions (Rex) PubMed
  • Regulatory mechanism: Rex: transcription repression PubMed
  • 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
Retrieved from "http://subtiwiki.uni-goettingen.de/wiki//index.php?title=Sandbox&oldid=54342"