Difference between revisions of "Sandbox"

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−
* '''Description:''' synthesis of spore killing factor <br/><br/>
+
* '''Description:''' ABC transporter (binding protein), export of the spore killing factor <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'''
−
|''skfD''
+
|''skfE''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ybcT''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ybdA''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
+
|style="background:#ABCDEF;" align="center"| '''Product''' || ABC transporter (binding protein)
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || synthesis of spore killing factor
+
|style="background:#ABCDEF;" align="center"|'''Function''' || export of the spore killing factor SkfA
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 34 kDa, 7.198  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 26 kDa, 6.34  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 933 bp, 311 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 717 bp, 239 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[skfC]]'', ''[[skfE]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[skfD]]'', ''[[skfF]]''
 
|-
 
|-
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/ybcT_nucleotide.txt    Gene sequence      (+200bp)  ]'''
+
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB11989&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/ybcT_protein.txt Protein sequence]'''
 
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:ybcT_context.gif]]
+
|-
 +
|-
 +
|colspan="2" | '''Genetic context''' <br/> [[Image:ybdA_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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=== Basic information ===
 
=== Basic information ===
  
−
* '''Locus tag:''' BSU01940
+
* '''Locus tag:''' BSU01950
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
Line 42: Line 43:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/skf.html]
+
* '''DBTBS entry:''' no entry
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12717]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12718]
  
 
=== Additional information===
 
=== Additional information===
Line 53: Line 54:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:'''  
+
* '''Catalyzed reaction/ biological activity:''' ATP + H<sub>2</sub>O + sulfate(Out) = ADP + phosphate + sulfate(In) (according to Swiss-Prot)
  
−
* '''Protein family:'''
+
* '''Protein family:''' ABC transporter domain (according to Swiss-Prot)
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
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* '''Interactions:'''
 
* '''Interactions:'''
  
−
* '''Localization:''' membrane (according to Swiss-Prot)
+
* '''Localization:''' cell membrane (according to Swiss-Prot)
  
 
=== Database entries ===
 
=== Database entries ===
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* '''Structure:'''
 
* '''Structure:'''
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/O31426 O31426]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/O31427 O31427]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU01940]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU01950]
  
−
* '''E.C. number:'''
+
* '''E.C. number:''' [http://www.expasy.org/enzyme/3.6.3.25 3.6.3.25]
  
 
=== Additional information===
 
=== Additional information===

Revision as of 14:48, 11 June 2009

  • Description: ABC transporter (binding protein), export of the spore killing factor

Gene name skfE
Synonyms ybdA
Essential no
Product ABC transporter (binding protein)
Function export of the spore killing factor SkfA
MW, pI 26 kDa, 6.34
Gene length, protein length 717 bp, 239 aa
Immediate neighbours skfD, skfF
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
YbdA context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Locus tag: BSU01950

Phenotypes of a mutant

Database entries

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

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity: ATP + H2O + sulfate(Out) = ADP + phosphate + sulfate(In) (according to Swiss-Prot)
  • Protein family: ABC transporter domain (according to Swiss-Prot)
  • Paralogous protein(s):

Extended information on the protein

  • Kinetic information:
  • Domains:
  • Modification:
  • Cofactor(s):
  • Effectors of protein activity:
  • Interactions:
  • Localization: cell membrane (according to Swiss-Prot)

Database entries

  • Structure:
  • KEGG entry: [2]

Additional information

Expression and regulation

  • Regulation:
  • Regulatory mechanism:
  • Additional information: Northern blotting during during phosphate limitation showed an intense 0.25 kb skfA-specific transcript, and a weaker 6.5 kb skfA-skfB-skfC-skfD-skfE-skfF-skfG-skfH transcript. PubMed

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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