Difference between revisions of "YmdB"

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(References)
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|style="background:#ABCDEF;" align="center"|'''Function''' || control of bistable gene expression
 
|style="background:#ABCDEF;" align="center"|'''Function''' || control of bistable gene expression
 
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|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU16970 ymdB]
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|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU16970 ymdB]
 
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|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 29,1 kDa, 6.50
 
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 29,1 kDa, 6.50
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|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[rny]]'', ''[[spoVS]]''
 
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[rny]]'', ''[[spoVS]]''
 
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|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB13570&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
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|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU16970 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU16970 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU16970 Advanced_DNA]
 
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|colspan="2" | '''Genetic context''' <br/> [[Image:ymdB_context.gif]]
 
|colspan="2" | '''Genetic context''' <br/> [[Image:ymdB_context.gif]]

Revision as of 12:53, 13 May 2013

  • Description: phosphodiesterase, controls bistable gene expression

Gene name ymdB
Synonyms
Essential no
Product phosphodiesterase
Function control of bistable gene expression
Gene expression levels in SubtiExpress: ymdB
MW, pI 29,1 kDa, 6.50
Gene length, protein length 792 bp, 264 amino acids
Immediate neighbours rny, spoVS
Sequences Protein DNA Advanced_DNA
Genetic context
YmdB context.gif
This image was kindly provided by SubtiList
Expression at a glance   PubMed
YmdB expression.png















Categories containing this gene/protein

biofilm formation

This gene is a member of the following regulons

The gene

Basic information

  • Locus tag: BSU16970

Phenotypes of a mutant

Database entries

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

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity: phosphatase activity toward phosphoenolpyruvate and phosphodiesterase activity toward 2',3'-cAMP (the Deinococcus ortholog) PubMed
  • Protein family:
  • Paralogous protein(s):

Extended information on the protein

  • Kinetic information:
  • Domains:
  • Modification:
  • Cofactor(s):
  • Effectors of protein activity:

Database entries

  • Structure: 1T70 (the protein of Deinococcus radiodurans, 44% identity) PubMed
  • KEGG entry: [2]
  • E.C. number:

Additional information

Expression and regulation

  • Regulation: constitutive
  • Regulatory mechanism:
  • Additional information: there is a terminator between rny and ymdB, most transcripts terminate there PubMed

Biological materials

  • Mutant:
    • GP583 (spc), available in Stülke lab
    • GP922 (cat), available in Stülke lab
    • GP921 (spc) NCIB3610 derivate, available in Stülke lab
    • GP969 (ymdB(E39Q)-cat) inactive enzyme, available in Stülke lab
  • Expression vector:
    • for expression/ purification from B. subtilis with N-terminal Strep-tag, for SPINE, in pGP380: pGP1041, available in Stülke lab
    • for expression/ purification from B. subtilis with C-terminal Strep-tag, for SPINE, in pGP382: pGP1919, available in Stülke lab
    • for expression/ purification from E. coli with N-terminal His-tag, in pWH844: pGP1040, available in Stülke lab
    • for expression/ purification from E. coli with N-terminal Strep-tag, in pGP172: pGP1917, available in Stülke lab
    • GP970 (ymdB-Strep (cat)), purification from B. subtilis, for SPINE, available in Stülke lab
  • lacZ fusion:
  • GFP fusion:
  • two-hybrid system: B. pertussis adenylate cyclase-based bacterial two hybrid system (BACTH), available in Stülke lab
  • FLAG-tag construct: GP1018 (spc, based on pGP1331), available in the Stülke lab
  • Antibody:

Labs working on this gene/protein

Jörg Stülke, University of Göttingen, Germany Homepage

Your additional remarks

References

Functional and structural analysis of orthologs in other organisms