Difference between revisions of "Sandbox"

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Line 1: Line 1:
−
* '''Description:''' serine protease Do (heat-shock protein) <br/><br/>
+
* '''Description:''' unknown <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'''
−
|''htrA''
+
|''ynzC''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ykdA ''
+
|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''' || serine protease Do (heat-shock protein)
+
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || probably involved in processing, maturation, or secretion of extracellular enzymes
+
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 47 kDa, 4.699  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 8 kDa, 10.285  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1347 bp, 449 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 231 bp, 77 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ykcC]]'', ''[[proG]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yneB]]'', ''[[tkt]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB13147&#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:CAB13672&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|-
+
|colspan="2" | '''Genetic context''' <br/> [[Image:ynzC_context.gif]]
−
|-
 
−
|colspan="2" | '''Genetic context''' <br/> [[Image:htrA_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 37: Line 35:
 
=== Basic information ===
 
=== Basic information ===
  
−
* '''Locus tag:''' BSU12900
+
* '''Locus tag:''' BSU17880
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
Line 43: Line 41:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/htrA.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yneAB-ynzC.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12608]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13466]
  
 
=== Additional information===
 
=== Additional information===
Line 56: Line 54:
 
* '''Catalyzed reaction/ biological activity:'''  
 
* '''Catalyzed reaction/ biological activity:'''  
  
−
* '''Protein family:''' PDZ (DHR) domain (according to Swiss-Prot)
+
* '''Protein family:''' UPF0291 family (according to Swiss-Prot)
  
−
* '''Paralogous protein(s):''' [[YyxA]]
+
* '''Paralogous protein(s):'''
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
Line 74: Line 72:
 
* '''Interactions:'''
 
* '''Interactions:'''
  
−
* '''Localization:''' cell membrane (according to Swiss-Prot),  extracellular (signal peptide) [http://www.ncbi.nlm.nih.gov/pubmed/18957862 PubMed]
+
* '''Localization:''' cytoplasm (according to Swiss-Prot)
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''Structure:'''
+
* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=2HEP 2HEP] (NMR),  [http://www.rcsb.org/pdb/explore.do?structureId=3BHP 3BHP]
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/O34358 O34358]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/O31818 O31818]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU12900]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU17880]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
Line 92: Line 90:
 
* '''Operon:'''  
 
* '''Operon:'''  
  
−
* '''[[Sigma factor]]:'''  
+
* '''[[[[Sigma factor]]]]:'''  
  
 
* '''Regulation:'''  
 
* '''Regulation:'''  
Line 120: Line 118:
 
=References=
 
=References=
  
−
<pubmed>12850135, </pubmed>
+
<pubmed>8000527,12123463,18487328,10941796,18757537,1904524,16547058,14523131, </pubmed>
−
# Voigt et al. (2009) Cell physiology and protein secretion of ''Bacillus licheniformis'' compared to ''Bacillus subtilis''. ''J Mol Microbiol Biotechnol.'' '''16:''' 53-68 [http://www.ncbi.nlm.nih.gov/pubmed/18957862 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 12:58, 8 June 2009

  • Description: unknown

Gene name ynzC
Synonyms
Essential no
Product unknown
Function unknown
MW, pI 8 kDa, 10.285
Gene length, protein length 231 bp, 77 aa
Immediate neighbours yneB, tkt
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
YnzC context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Locus tag: BSU17880

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: UPF0291 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

  • KEGG entry: [3]
  • E.C. number:

Additional information

Expression and regulation

  • Operon:
  • Regulation:
  • 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

Kalpana D Singh, Matthias H Schmalisch, Jörg Stülke, Boris Görke
Carbon catabolite repression in Bacillus subtilis: quantitative analysis of repression exerted by different carbon sources.
J Bacteriol: 2008, 190(21);7275-84
[PubMed:18757537] [WorldCat.org] [DOI] (I p)

Jeffrey G Gardner, Jorge C Escalante-Semerena
Biochemical and mutational analyses of AcuA, the acetyltransferase enzyme that controls the activity of the acetyl coenzyme a synthetase (AcsA) in Bacillus subtilis.
J Bacteriol: 2008, 190(14);5132-6
[PubMed:18487328] [WorldCat.org] [DOI] (I p)

Naoya Terahara, Makoto Fujisawa, Benjamin Powers, Tina M Henkin, Terry A Krulwich, Masahiro Ito
An intergenic stem-loop mutation in the Bacillus subtilis ccpA-motPS operon increases motPS transcription and the MotPS contribution to motility.
J Bacteriol: 2006, 188(7);2701-5
[PubMed:16547058] [WorldCat.org] [DOI] (P p)

Ingrid Wacker, Holger Ludwig, Irene Reif, Hans-Matti Blencke, Christian Detsch, Jörg Stülke
The regulatory link between carbon and nitrogen metabolism in Bacillus subtilis: regulation of the gltAB operon by the catabolite control protein CcpA.
Microbiology (Reading): 2003, 149(Pt 10);3001-3009
[PubMed:14523131] [WorldCat.org] [DOI] (P p)

Holger Ludwig, Nicole Rebhan, Hans-Matti Blencke, Matthias Merzbacher, Jörg Stülke
Control of the glycolytic gapA operon by the catabolite control protein A in Bacillus subtilis: a novel mechanism of CcpA-mediated regulation.
Mol Microbiol: 2002, 45(2);543-53
[PubMed:12123463] [WorldCat.org] [DOI] (P p)

N Faires, S Tobisch, S Bachem, I Martin-Verstraete, M Hecker, J Stülke
The catabolite control protein CcpA controls ammonium assimilation in Bacillus subtilis.
J Mol Microbiol Biotechnol: 1999, 1(1);141-8
[PubMed:10941796] [WorldCat.org] (P p)

Y Miwa, M Saikawa, Y Fujita
Possible function and some properties of the CcpA protein of Bacillus subtilis.
Microbiology (Reading): 1994, 140 ( Pt 10);2567-75
[PubMed:8000527] [WorldCat.org] [DOI] (P p)

T M Henkin, F J Grundy, W L Nicholson, G H Chambliss
Catabolite repression of alpha-amylase gene expression in Bacillus subtilis involves a trans-acting gene product homologous to the Escherichia coli lacl and galR repressors.
Mol Microbiol: 1991, 5(3);575-84
[PubMed:1904524] [WorldCat.org] [DOI] (P p)

  1. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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