Difference between revisions of "Sandbox"

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−
* '''Description:''' two-component response regulator, regulation of phosphate metabolism <br/><br/>
+
* '''Description:''' inhibitor of AbrB activity<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'''
−
|''phoP''
+
|''abbA ''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ykzF''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || two-component response regulator
+
|style="background:#ABCDEF;" align="center"| '''Product''' || anti-repressor
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || regulation of phosphate metabolism <br/>(phoA, phoB, phoD, resABCDE, tagAB, tagDEF, tuaA-H)
+
|style="background:#ABCDEF;" align="center"|'''Function''' || inhibition of AbrB
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 27 kDa, 5.068  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 7 kDa, 4.642  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 720 bp, 240 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 195 bp, 65 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[phoR]]'', ''[[mdh]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ykuK]]'', ''[[ykuL]]''
 
|-
 
|-
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/phoP_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/ykzF_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/phoP_protein.txt Protein sequence]'''
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/ykzF_protein.txt Protein sequence]'''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;color:#FF0000" align="center" | '''Caution: The sequence for this gene in SubtiList contains errors
+
|colspan="2" | '''Genetic context''' <br/> [[Image:ykzF_context.gif]]
−
|-
 
−
|colspan="2" | '''Genetic context''' <br/> [[Image:phoP_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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__TOC__
 
__TOC__
  
−
<br/><br/><br/><br/>
+
<br/><br/>
  
 
=The gene=
 
=The gene=
Line 44: Line 42:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/phoPR.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ykuJK-ykzF-ykuL-ccpC.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10363]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13334]
  
 
=== Additional information===
 
=== Additional information===
Line 55: Line 53:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:'''  
+
* '''Catalyzed reaction/ biological activity:''' inhibition of AbrB activity [http://www.ncbi.nlm.nih.gov/sites/entrez/18840696 PubMed]
  
 
* '''Protein family:'''
 
* '''Protein family:'''
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
−
 
−
=== Genes controlled by PhoP ===
 
−
 
−
* '''Activation by PhoP:''' ''[[phoP]]-[[phoR]]''
 
−
 
−
* '''Repression by PhoP:'''
 
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
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* '''Domains:'''  
 
* '''Domains:'''  
  
−
* '''Modification:''' phosphorylation by [[PhoR]] under conditions of phosphate limitation (stimulates DNA-binding activity)
+
* '''Modification:'''
  
 
* '''Cofactor(s):'''
 
* '''Cofactor(s):'''
Line 79: Line 71:
 
* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
  
−
* '''Interactions:''' [[PhoP]]-[[PhoR]]
+
* '''Interactions:''' AbbA-[[AbrB]] [http://www.ncbi.nlm.nih.gov/sites/entrez/18840696 PubMed]
  
 
* '''Localization:'''
 
* '''Localization:'''
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* '''Swiss prot entry:'''
 
* '''Swiss prot entry:'''
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU29110]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU14120]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
Line 97: Line 89:
 
=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''[[phoP]]-[[phoR]]''
+
* '''Operon:'''  
  
−
* '''Sigma factor:''' [[SigA]]
+
* '''Sigma factor:'''  
  
−
* '''Regulation:''' repressed by glucose (4.3-fold) ([[CcpA]]) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed],  induced by phosphate limitation ([[PhoP]]), carbon catabolite repression ([[CcpA]])
+
* '''Regulation:''' repressed by glucose (4.3-fold) ([[CcpA]]) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed],  subject to carbon catabolite repression (4-fold: [[CcpA]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/12850135 PubMed], expressed at onset of stationary phase ([[Spo0A]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/18840696 PubMed]
  
−
* '''Regulatory mechanism:''' [[CcpA]]: transcription repression,  [[PhoP]]: transcription activation, [[CcpA]]: transcription repression
+
* '''Regulatory mechanism:''' [[CcpA]]: transcription repression,  [[CcpA]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/12850135 PubMed], [[Spo0A]]: transcription activation by Spo0A~P [http://www.ncbi.nlm.nih.gov/sites/entrez/18840696 PubMed]
  
 
* '''Additional information:'''
 
* '''Additional information:'''
Line 122: Line 114:
  
 
=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
 +
 +
[[Richard Losick]], Harvard Univ., Cambridge, USA [http://www.mcb.harvard.edu/Losick/ homepage]
  
 
=Your additional remarks=
 
=Your additional remarks=
Line 128: Line 122:
  
 
# Blencke et al. (2003) Transcriptional profiling of gene expression in response to glucose in ''Bacillus subtilis'': regulation of the central metabolic pathways. ''Metab Eng.'' '''5:''' 133-149 [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]
 
# Blencke et al. (2003) Transcriptional profiling of gene expression in response to glucose in ''Bacillus subtilis'': regulation of the central metabolic pathways. ''Metab Eng.'' '''5:''' 133-149 [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]
 +
# Banse et al. (2008) Parallel pathways of repression and antirepression governing the transition to stationary phase in ''Bacillus subtilis''.''Proc. Natl. Acad. Sci. USA'' '''105:''' 15547-15552. [http://www.ncbi.nlm.nih.gov/sites/entrez/18840696 PubMed]
 +
# Blencke, H.-M., Homuth, G., Ludwig, H., Mäder, U., Hecker, M. & Stülke, J. (2003) Transcriptional profiling of gene expression in response to glucose in Bacillus subtilis: regulation of the central metabolic pathways. Metab. Engn. 5: 133-149. [http://www.ncbi.nlm.nih.gov/sites/entrez/12850135 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 10:02, 6 April 2009

  • Description: inhibitor of AbrB activity

Gene name abbA
Synonyms ykzF
Essential no
Product anti-repressor
Function inhibition of AbrB
MW, pI 7 kDa, 4.642
Gene length, protein length 195 bp, 65 aa
Immediate neighbours ykuK, ykuL
Gene sequence (+200bp) Protein sequence
Genetic context
YkzF 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: inhibition of AbrB activity PubMed
  • Protein family:
  • Paralogous protein(s):

Extended information on the protein

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

Database entries

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

Additional information

Expression and regulation

  • Operon:
  • Sigma factor:
  • Regulation: repressed by glucose (4.3-fold) (CcpA) PubMed, subject to carbon catabolite repression (4-fold: CcpA) PubMed, expressed at onset of stationary phase (Spo0A) PubMed
  • Regulatory mechanism: CcpA: transcription repression, CcpA: transcription repression PubMed, Spo0A: transcription activation by Spo0A~P PubMed
  • Additional information:

Biological materials

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

Labs working on this gene/protein

Richard Losick, Harvard Univ., Cambridge, USA homepage

Your additional remarks

References

  1. Blencke et al. (2003) Transcriptional profiling of gene expression in response to glucose in Bacillus subtilis: regulation of the central metabolic pathways. Metab Eng. 5: 133-149 PubMed
  2. Banse et al. (2008) Parallel pathways of repression and antirepression governing the transition to stationary phase in Bacillus subtilis.Proc. Natl. Acad. Sci. USA 105: 15547-15552. PubMed
  3. Blencke, H.-M., Homuth, G., Ludwig, H., Mäder, U., Hecker, M. & Stülke, J. (2003) Transcriptional profiling of gene expression in response to glucose in Bacillus subtilis: regulation of the central metabolic pathways. Metab. Engn. 5: 133-149. PubMed
  4. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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