Difference between revisions of "Sandbox"

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* '''Description:''' transcriptional activator of maltose utilization <br/><br/>
+
* '''Description:''' glucomannan-specific phosphotransferase system, EIIA component <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'''
−
|''glvR''
+
|''gmuA''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yfiA''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ydhN''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || transcriptional activator
+
|style="background:#ABCDEF;" align="center"| '''Product''' || glucomannan-specific phosphotransferase system, EIIA component
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || regulation of maltose utilization
+
|style="background:#ABCDEF;" align="center"|'''Function''' || glucomannan uptake and phosphorylation
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 29 kDa, 5.446  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 12 kDa, 5.63  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 762 bp, 254 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 330 bp, 110 aa  
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[malA]]'', ''[[malP]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[gmuB]]'', ''[[gmuC]]''
 
|-
 
|-
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/yfiA_nucleotide.txt    Gene sequence      (+200bp)  ]'''
+
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB12401&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/yfiA_protein.txt Protein sequence]'''
 
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:yfiA_context.gif]]
+
|-
 +
|-
 +
|colspan="2" | '''Genetic context''' <br/> [[Image:ydhN_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:''' BSU08190
+
* '''Locus tag:''' BSU05820
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
Line 42: Line 43:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/malA-yfiA-malP.html]
+
* '''DBTBS entry:''' no entry
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11847]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12191]
  
 
=== Additional information===
 
=== Additional information===
Line 55: Line 56:
 
* '''Catalyzed reaction/ biological activity:'''  
 
* '''Catalyzed reaction/ biological activity:'''  
  
−
* '''Protein family:'''
+
* '''Protein family:''' PTS permease, lactose permease (Lac) family [http://www.ncbi.nlm.nih.gov/pubmed/10627040 PubMed]
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
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* '''Structure:'''
 
* '''Structure:'''
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P54717 P54717]
+
* '''Swiss prot entry:'''
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU08190]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU05820]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
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=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''[[malA]]-[[glvR]]-[[malP]]''
+
* '''Operon:''' ''[[gmuB]]-[[gmuA]]-[[gmuC]]-[[gmuD]]-[[gmuR]]-[[gmuE]]-[[gmuF]]-[[gmuG]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/18177310 PubMed]
  
−
* '''Sigma factor:''' [[SigA]]
+
* '''[[Sigma factor]]:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/18177310 PubMed]
  
−
* '''Regulation:''' repressed by glucose ([[CcpA]])
+
* '''Regulation:'''  
 +
** induced by conjac glucomannan (requires [[GmuG]]) ([[GmuR]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/18177310 PubMed]
 +
** induced by cellobiose ([[GmuR]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/18177310 PubMed]
 +
** subject to carbon catabolite repression ([[CcpA]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/18177310 PubMed]
  
−
* '''Regulatory mechanism:''' [[CcpA]]: transcription repression  
+
* '''Regulatory mechanism:'''  
 +
** [[GmuR]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/18177310 PubMed]
 +
** [[CcpA]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/18177310 PubMed]
  
 
* '''Additional information:'''
 
* '''Additional information:'''
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=References=
 
=References=
  
−
<pubmed>11489864, </pubmed>
+
<pubmed>10627040 18177310, </pubmed>
−
 
+
# Reizer et al. (1999) Novel phosphotransferase system genes revealed by genome analysis - the complete complement of PTS proteins encoded within the genome of ''Bacillus subtilis''. ''Microbiology'' '''145:''' 3419-3429 [http://www.ncbi.nlm.nih.gov/pubmed/10627040 PubMed]
−
# Yamamoto H, Serizawa M, Thompson J, Sekiguchi J.(2001) Regulation of the ''glv'' operon in ''Bacillus subtilis'': YfiA (GlvR) is a positive regulator of the operon that is repressed through CcpA and cre. ''J Bacteriol.'' '''183:''' 5110-5121. [http://www.ncbi.nlm.nih.gov/sites/entrez/11489864 PubMed]
+
# Sadaie Y, Nakadate H, Fukui R, Yee LM, Asai K. (2008) Glucomannan utilization operon of Bacillus subtilis. ''FEMS Microbiol Lett.'' '''Feb;279(1):''' 103-9. [http://www.ncbi.nlm.nih.gov/sites/entrez/18177310 PubMed]
 +
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]

Revision as of 14:05, 8 June 2009

  • Description: glucomannan-specific phosphotransferase system, EIIA component

Gene name gmuA
Synonyms ydhN
Essential no
Product glucomannan-specific phosphotransferase system, EIIA component
Function glucomannan uptake and phosphorylation
MW, pI 12 kDa, 5.63
Gene length, protein length 330 bp, 110 aa
Immediate neighbours gmuB, gmuC
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
YdhN context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Locus tag: BSU05820

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: PTS permease, lactose permease (Lac) family PubMed
  • 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: [2]
  • E.C. number:

Additional information

Expression and regulation

  • 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

Yoshito Sadaie, Hisashi Nakadate, Reiko Fukui, Lii Mien Yee, Kei Asai
Glucomannan utilization operon of Bacillus subtilis.
FEMS Microbiol Lett: 2008, 279(1);103-9
[PubMed:18177310] [WorldCat.org] [DOI] (P p)

Jonathan Reizer, Steffi Bachem, Aiala Reizer, Maryvonne Arnaud, Milton H Saier, Jörg Stülke
Novel phosphotransferase system genes revealed by genome analysis - the complete complement of PTS proteins encoded within the genome of Bacillus subtilis.
Microbiology (Reading): 1999, 145 ( Pt 12);3419-3429
[PubMed:10627040] [WorldCat.org] [DOI] (P p)

  1. Reizer et al. (1999) Novel phosphotransferase system genes revealed by genome analysis - the complete complement of PTS proteins encoded within the genome of Bacillus subtilis. Microbiology 145: 3419-3429 PubMed
  2. Sadaie Y, Nakadate H, Fukui R, Yee LM, Asai K. (2008) Glucomannan utilization operon of Bacillus subtilis. FEMS Microbiol Lett. Feb;279(1): 103-9. PubMed
  3. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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