Difference between revisions of "Sandbox"

From SubtiWiki
Jump to: navigation, search
Line 1: Line 1:
−
* '''Description:''' serine hydroxymethyltransferase <br/><br/>
+
* '''Description:''' alkaline phosphatase A <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'''
−
|''glyA''
+
|''phoB''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''glyC, ipc-34d ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''phoAIII ''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
+
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || serine hydroxymethyltransferase
+
|style="background:#ABCDEF;" align="center"| '''Product''' || alkaline phosphatase A
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || biosynthesis of glycine
+
|style="background:#ABCDEF;" align="center"|'''Function''' || aquisition of phosphate upon phosphoate starvation
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 45 kDa, 5.475  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 50 kDa, 5.895  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1245 bp, 415 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1386 bp, 462 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[upp]]'', ''[[ywlG]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ydhF]]'', ''[[ydhG]]''
 
|-
 
|-
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/glyA_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/phoB_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/glyA_protein.txt Protein sequence]'''
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/phoB_protein.txt Protein sequence]'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:glyA_context.gif]]
+
|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:phoB_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 39: Line 41:
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
−
 
−
essential [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
 
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/glyA.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/phoB-ydhF.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10944]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10697]
  
 
=== Additional information===
 
=== Additional information===
Line 59: Line 59:
 
* '''Protein family:'''
 
* '''Protein family:'''
  
−
* '''Paralogous protein(s):'''
+
* '''Paralogous protein(s):''' [[PhoA]]
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
Line 83: Line 83:
 
* '''Swiss prot entry:'''
 
* '''Swiss prot entry:'''
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU36900]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU05740]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
Line 91: Line 91:
 
=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''[[glyA]]''
+
* '''Operon:''' ''[[phoB]]-[[ydhF]]''
  
−
* '''Sigma factor:''' [[SigA]]
+
* '''Sigma factor:''' [[SigA]], [[SigE]]
  
 
* '''Regulation:'''  
 
* '''Regulation:'''  

Revision as of 15:01, 31 March 2009

  • Description: alkaline phosphatase A

Gene name phoB
Synonyms phoAIII
Essential no
Product alkaline phosphatase A
Function aquisition of phosphate upon phosphoate starvation
MW, pI 50 kDa, 5.895
Gene length, protein length 1386 bp, 462 aa
Immediate neighbours ydhF, ydhG
Gene sequence (+200bp) Protein sequence
Caution: The sequence for this gene in SubtiList contains errors
Genetic context
PhoB 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:
  • Protein family:
  • Paralogous protein(s): PhoA

Extended information on the protein

  • Kinetic information:
  • Domains:
  • Modification: phosphorylated on ser/ thr/ tyr PubMed
  • Cofactor(s):
  • Effectors of protein activity:
  • Interactions:
  • Localization:

Database entries

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

Additional information

Expression and regulation

  • Regulation:
  • Regulatory mechanism:
  • 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. Lévine et al. (2006) Analysis of the dynamic Bacillus subtilis Ser/Thr/Tyr phosphoproteome implicated in a wide variety of cellular processes. Proteomics 6: 2157-2173 PubMed
  2. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
Retrieved from "http://subtiwiki.uni-goettingen.de/wiki//index.php?title=Sandbox&oldid=46068"