Difference between revisions of "Sandbox"

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−
* '''Description:''' anti-SigD, regulation of flagellin, motility, and chemotaxis <br/><br/>
+
* '''Description:''' two-component response regulator, regulation of degradative enzyme and genetic competence, involved in activation of capsule biosynthetic operon expression (together with [[SwrAA]]) <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'''
−
|''flgM''
+
|''degU''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''sacU, iep ''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
+
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || anti-SigD
+
|style="background:#ABCDEF;" align="center"| '''Product''' || two-component response regulator
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || control of SigD activity
+
|style="background:#ABCDEF;" align="center"|'''Function''' || regulation of degradative enzyme and genetic competence
 +
of genetic competence
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 9 kDa, 9.918  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 25 kDa, 5.602  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 264 bp, 88 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 687 bp, 229 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yvyG]]'', ''[[yvyF]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yviA]]'', ''[[degS]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB15560&#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:CAB15566&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:flgM_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:degU_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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=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/comFABC-yvyF-flgM-yvyG-flgKL.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/degSU.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10399]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10393]
  
 
=== Additional information===
 
=== Additional information===
Line 52: Line 53:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:'''  
+
* '''Catalyzed reaction/ biological activity:''' transcription activator of degradative enzyme genes (''[[sacB]]'' and ''[[degQ]]'') and of ''[[comK]]'' expression
  
 
* '''Protein family:'''
 
* '''Protein family:'''
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
 +
 +
=== Genes controlled by DegU ===
 +
 +
* '''Activation by DegU:''' ''[[degS]]-[[degU]]''
 +
 +
* '''Repression by DegU:'''
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
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* '''Domains:'''  
 
* '''Domains:'''  
  
−
* '''Modification:'''
+
* '''Modification:''' phosphorylation by [[DegS]] modulates DNA-binding activity
  
 
* '''Cofactor(s):'''
 
* '''Cofactor(s):'''
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* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
  
−
* '''Interactions:''' [[FlgM]]-[[SigD]],  
+
* '''Interactions:''' [[DegU]]-[[RapG]], [[DegS]]-[[DegU]]
  
 
* '''Localization:'''
 
* '''Localization:'''
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* '''Swiss prot entry:'''
 
* '''Swiss prot entry:'''
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU35430]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU35490]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
Line 88: Line 95:
 
=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:'''  
+
* '''Operon:''''' [[degS]]-[[degU]]''
  
−
* '''[[Sigma factor]]:'''  
+
* '''[[Sigma factor]]:''' [[SigA]]
  
−
* '''Regulation:'''  
+
* '''Regulation:''' induced in the presence of ammonium ([[TnrA]])
  
−
* '''Regulatory mechanism:'''  
+
* '''Regulatory mechanism:''' [[TnrA]]: repression, [[DegU]]: positive autoregulation
  
−
* '''Additional information:'''  
+
* '''Additional information:'''
  
 
=Biological materials =
 
=Biological materials =

Revision as of 00:23, 28 April 2009

  • Description: two-component response regulator, regulation of degradative enzyme and genetic competence, involved in activation of capsule biosynthetic operon expression (together with SwrAA)

Gene name degU
Synonyms sacU, iep
Essential no
Product two-component response regulator
Function regulation of degradative enzyme and genetic competence

of genetic competence

MW, pI 25 kDa, 5.602
Gene length, protein length 687 bp, 229 aa
Immediate neighbours yviA, degS
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
DegU 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: transcription activator of degradative enzyme genes (sacB and degQ) and of comK expression
  • Protein family:
  • Paralogous protein(s):

Genes controlled by DegU

  • Repression by DegU:

Extended information on the protein

  • Kinetic information:
  • Domains:
  • Modification: phosphorylation by DegS modulates DNA-binding activity
  • Cofactor(s):
  • Effectors of protein activity:
  • Localization:

Database entries

  • Structure:
  • Swiss prot entry:
  • KEGG entry: [3]
  • E.C. number:

Additional information

Expression and regulation

  • Regulation: induced in the presence of ammonium (TnrA)
  • Regulatory mechanism: TnrA: repression, DegU: positive autoregulation
  • 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
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