Difference between revisions of "Sandbox"

From SubtiWiki
Jump to: navigation, search
Line 1: Line 1:
−
* '''Description:''' endopeptidase-type autolysin <br/><br/>
+
* '''Description:''' adenylyl-sulfate kinase <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'''
−
|''cwlO''
+
|''cysC''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yzkA, yvcE ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ylnC ''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || endopeptidase-type autolysin
+
|style="background:#ABCDEF;" align="center"| '''Product''' || adenylyl-sulfate kinase
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || cell wall synthesis
+
|style="background:#ABCDEF;" align="center"|'''Function''' || sulfate reduction and activation
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 50 kDa, 5.326  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 22 kDa, 5.083  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1419 bp, 473 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 591 bp, 197 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[trxB]]'', ''[[yvcD]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[sat]]'', ''[[ylnD]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB15485&#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:CAB13434&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:yvcE_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:cysC_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 35: Line 35:
 
=== Basic information ===
 
=== Basic information ===
  
−
* '''Locus tag:''' BSU34800
+
* '''Locus tag:''' BSU15600
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
Line 41: Line 41:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' no entry
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/cysHP-sat-cysC-ylnDEF.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11023]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13379]
  
 
=== Additional information===
 
=== Additional information===
Line 52: Line 52:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:'''  
+
* '''Catalyzed reaction/ biological activity:''' ATP + adenylyl sulfate = ADP + 3'-phosphoadenylyl sulfate (according to Swiss-Prot)
  
−
* '''Protein family:''' peptidase C40 family (according to Swiss-Prot)
+
* '''Protein family:''' APS kinase family (according to Swiss-Prot)
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
Line 72: Line 72:
 
* '''Interactions:'''
 
* '''Interactions:'''
  
−
* '''Localization:''' secreted (according to Swiss-Prot),  extracellular (signal peptide) [http://www.ncbi.nlm.nih.gov/pubmed/18957862 PubMed]
+
* '''Localization:'''
  
 
=== Database entries ===
 
=== Database entries ===
Line 78: Line 78:
 
* '''Structure:'''
 
* '''Structure:'''
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P40767 P40767]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/O34577 O34577]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU34800]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU15600]
  
−
* '''E.C. number:'''
+
* '''E.C. number:''' [http://www.expasy.org/enzyme/2.7.1.25 2.7.1.25]
  
 
=== Additional information===
 
=== Additional information===
Line 88: Line 88:
 
=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:'''  
+
* '''Operon:''' ''[[cysH]]-[[cysP]]-[[sat]]-[[cysC]]-[[ylnD]]-[[ylnE]]-[[ylnF]]''
  
−
* '''[[Sigma factor]]:'''  
+
* '''[[Sigma factor]]:''' [[SigA]]
  
−
* '''Regulation:''' activated by [[WalR]] [http://www.ncbi.nlm.nih.gov/sites/entrez/17581128 PubMed]
+
* '''Regulation:'''  
 +
** repressed by casamino acids [http://www.ncbi.nlm.nih.gov/pubmed/12107147 PubMed]
 +
** repressed in the presence of cysteine ([[CymR]])
 +
** induced by methionine starvation ([[S-box]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/10094622 PubMed]
  
 
* '''Regulatory mechanism:'''  
 
* '''Regulatory mechanism:'''  
 +
** [[S-box]]: transcription termination/ antitermination, the [[S-box]] [[riboswitch]] binds S-adenosylmethionine resulting in termination [http://www.ncbi.nlm.nih.gov/sites/entrez/10094622 PubMed]
 +
** [[CymR]]: transcription repression
  
 
* '''Additional information:'''
 
* '''Additional information:'''
Line 113: Line 118:
  
 
=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
 +
 +
[[Isabelle Martin-Verstraete]], Institute Pasteur, Paris, France
  
 
=Your additional remarks=
 
=Your additional remarks=
Line 118: Line 125:
 
=References=
 
=References=
  
−
<pubmed>18957862, </pubmed>
+
<pubmed>12107147, </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]
+
# 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]
 
# 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 14:01, 8 June 2009

  • Description: adenylyl-sulfate kinase

Gene name cysC
Synonyms ylnC
Essential no
Product adenylyl-sulfate kinase
Function sulfate reduction and activation
MW, pI 22 kDa, 5.083
Gene length, protein length 591 bp, 197 aa
Immediate neighbours sat, ylnD
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
CysC context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Locus tag: BSU15600

Phenotypes of a mutant

Database entries

  • DBTBS entry: [1]
  • SubtiList entry: [2]

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity: ATP + adenylyl sulfate = ADP + 3'-phosphoadenylyl sulfate (according to Swiss-Prot)
  • Protein family: APS kinase 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:

Database entries

  • Structure:
  • KEGG entry: [3]

Additional information

Expression and regulation

  • Regulation:
    • repressed by casamino acids PubMed
    • repressed in the presence of cysteine (CymR)
    • induced by methionine starvation (S-box) PubMed
  • Regulatory mechanism:
    • S-box: transcription termination/ antitermination, the S-box riboswitch binds S-adenosylmethionine resulting in termination PubMed
    • CymR: transcription repression
  • Additional information:

Biological materials

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

Labs working on this gene/protein

Isabelle Martin-Verstraete, Institute Pasteur, Paris, France

Your additional remarks

References

  1. Mäder et al. (2002) Transcriptome and Proteome Analysis of Bacillus subtilis Gene Expression Modulated by Amino Acid Availability. J. Bacteriol 184: 1844288-4295 PubMed
  2. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
Retrieved from "http://subtiwiki-test.uni-goettingen.de/wiki//index.php?title=Sandbox&oldid=89095"