Difference between revisions of "Sandbox"

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−
* '''Description:''' fructose 1,6-bisphosphate aldolase, glycolytic/ gluconeogenic enzyme<br/><br/>
+
* '''Description:''' write here <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'''
−
|''fbaA''
+
|''ahpF''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''fba, fba1, tsr ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ndh ''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes
+
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"| '''Product''' || fructose-1,6-bisphosphate aldolase
+
|style="background:#ABCDEF;" align="center"| '''Product''' || alkyl hydroperoxide reductase (large subunit) and NADH dehydrogenase (EC 1.6.99.3)
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || enzyme in glycolysis/ gluconeogenesis
+
|style="background:#ABCDEF;" align="center"|'''Function''' ||  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 30,2 kDa, 5.03
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 54 kDa, 4.705 
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 855 bp, 285 amino acids
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1527 bp, 509 aa
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[spo0F]]'', ''[[ywjH]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ahpC]]'', ''[[bglA]]''
 
|-
 
|-
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/fbaA_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/ahpF_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/fbaA_protein.txt Protein sequence]'''
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/ahpF_protein.txt Protein sequence]'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:fbaA_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:ahpF_context.gif]]
 
|-
 
|-
 
|}
 
|}
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<br/><br/>
 
<br/><br/>
−
 
  
 
=The gene=
 
=The gene=
Line 36: Line 35:
 
=== Basic information ===
 
=== Basic information ===
  
−
* '''Coordinates:''' 3807538 - 3808392
+
* '''Coordinates:'''
  
 
===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/fbaA-ywjH.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ahpCF.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10412]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11204]
  
 
=== Additional information===
 
=== Additional information===
 +
  
 
=The protein=
 
=The protein=
Line 54: Line 52:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:''' D-fructose 1,6-bisphosphate = dihydroxyacetone phosphate + D-glyceraldehyde 3-phosphate
+
* '''Catalyzed reaction/ biological activity:'''  
  
−
* '''Protein family:''' class II fructose-bisphosphate aldolase family.
+
* '''Protein family:'''
  
−
* '''Paralogous protein(s):''' [[FbaB]]
+
* '''Paralogous protein(s):'''
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
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* '''Domains:'''  
 
* '''Domains:'''  
−
** 2 x Dihydroxyacetone phosphate binding domain (210–212), (231–234)
 
  
−
* '''Modification:''' phosphorylation on Thr-212 AND Thr-234 [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed]
+
* '''Modification:''' phosphorylation on (Ser-48 OR Ser-49) [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed]
  
−
* '''Cofactor(s):''' 2 x zinc ion
+
* '''Cofactor(s):'''
  
−
* '''Effectors of protein activity:''' inhibited by alpha-keto acids [http://www.ncbi.nlm.nih.gov/pubmed/24624 PubMed]
+
* '''Effectors of protein activity:'''
  
 
* '''Interactions:'''
 
* '''Interactions:'''
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* '''Structure:'''
 
* '''Structure:'''
  
−
* '''Swiss prot entry:''' [http://www.expasy.ch/cgi-bin/sprot-search-ac?P13243]
+
* '''Swiss prot entry:'''
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU37120]
+
* '''KEGG entry:'''
  
−
* '''E.C. number:''' [http://www.expasy.org/enzyme/4.1.2.13]
+
* '''E.C. number:'''
  
 
=== Additional information===
 
=== Additional information===
−
 
−
Binds 2 zinc ions per subunit. One is catalytic and the other provides a structural contribution
 
  
 
=Expression and regulation=
 
=Expression and regulation=
  
 
* '''Operon:'''  
 
* '''Operon:'''  
−
**''fbaA'' [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+11489127 PubMed]
 
−
**''fbaA-[[ywjH]]'' [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+11489127 PubMed]
 
  
 
* '''Sigma factor:'''  
 
* '''Sigma factor:'''  
  
−
* '''Regulation:''' constitutively expressed [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+11489127 PubMed]
+
* '''Regulation:'''  
  
 
* '''Regulatory mechanism:'''  
 
* '''Regulatory mechanism:'''  
  
−
* '''Additional information:'''
+
* '''Additional information:'''  
  
 
=Biological materials =
 
=Biological materials =
  
−
* '''Mutant:'''  
+
* '''Mutant:'''
  
−
* '''Expression vector:''' pGP395 (N-terminal His-tag, in [[pWH844]]), pGP88 (N-terminal Strep-tag, for SPINE, expression in ''B. subtilis'', in [[pGP380]])
+
* '''Expression vector:'''
−
+
       
−
* '''lacZ fusion:''' pGP601 (in [[pAC6]])
+
* '''lacZ fusion:'''
  
 
* '''GFP fusion:'''
 
* '''GFP fusion:'''
  
−
* '''two-hybrid system:''' ''B. pertussis'' adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Stülke]] lab
+
* '''two-hybrid system:'''  
  
 
* '''Antibody:'''
 
* '''Antibody:'''
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=References=
 
=References=
 +
# Macek et al. (2007) The serine/ threonine/ tyrosine phosphoproteome of the model  bacterium ''Bacillus subtilis''. Mol. Cell. Proteomics 6: 697-707  [http://www.ncbi.nlm.nih.gov/pubmed/17218307 PubMed]
  
−
# Trach K, Chapman JW & Piggot P (1988) Complete sequence and transcriptional analysis of the ''spo0F'' region of the ''Bacillus subtilis'' chromosome  ''J Bacteriol.'' '''170:''' 4194-4208. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+2457578 PubMed]
+
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]
−
# Ludwig H, Homuth G & Schmalisch M (2001) Transcription of glycolytic genes and operons in ''Bacillus subtilis'': evidence for the presence of multiple levels of control of the ''gapA'' operon  ''Mol Microbiol.''  '''41:''' 409-422. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+11489127 PubMed]
 
−
# Macek et al. (2007) The serine/ threonine/ tyrosine phosphoproteome of the model  bacterium ''Bacillus subtilis''. Mol. Cell. Proteomics 6: 697-707  [http://www.ncbi.nlm.nih.gov/pubmed/17218307 PubMed]
 

Revision as of 15:25, 13 March 2009

  • Description: write here

Gene name ahpF
Synonyms ndh
Essential no
Product alkyl hydroperoxide reductase (large subunit) and NADH dehydrogenase (EC 1.6.99.3)
Function
MW, pI 54 kDa, 4.705
Gene length, protein length 1527 bp, 509 aa
Immediate neighbours ahpC, bglA
Gene sequence (+200bp) Protein sequence
Genetic context
AhpF context.gif



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):

Extended information on the protein

  • Kinetic information:
  • Domains:
  • Modification: phosphorylation on (Ser-48 OR Ser-49) PubMed
  • Cofactor(s):
  • Effectors of protein activity:
  • Interactions:
  • Localization:

Database entries

  • Structure:
  • Swiss prot entry:
  • KEGG entry:
  • E.C. number:

Additional information

Expression and regulation

  • Operon:
  • Sigma factor:
  • 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. Macek et al. (2007) The serine/ threonine/ tyrosine phosphoproteome of the model bacterium Bacillus subtilis. Mol. Cell. Proteomics 6: 697-707 PubMed
  1. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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