Difference between revisions of "SubtiPathways"

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=== [http://subtiwiki.uni-goettingen.de/pathways/cys_meth_and_sulfate_assimilation.html Sulfate assimilation] ===
 
=== [http://subtiwiki.uni-goettingen.de/pathways/cys_meth_and_sulfate_assimilation.html Sulfate assimilation] ===
  
=== [http://subtiwiki.uni-goettingen.de/pathways/tRNA_charging.html tRNA charging] ===
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=== [http://subtiwiki.uni-goettingen.de/subtipathways/index.php?pathway=trna tRNA charging] ===
  
 
=== [http://subtiwiki.uni-goettingen.de/pathways/biofilm.html Biofilm formation] ===
 
=== [http://subtiwiki.uni-goettingen.de/pathways/biofilm.html Biofilm formation] ===

Revision as of 14:58, 30 January 2014

Pathway start page small.png
legend for SubtiPathways
graphical notation: click to enlarge

SubtiPathways is a model of B. subtilis metabolism and regulation in SBML/SBGN (Systems Biology Markup Language/ Graphical Notation). There is a color code for key metabolites (see the legend on the right side).

It can be used like Google Maps (scroll and zoom to the pathways). The markers of proteins and compounds listed on the right side in each pathway are containing links to the corresponding SubtiWiki and PubChem pages, respectively. There is a short description for each protein in the bubbles, too.

Contact: General Microbiology, University of Göttingen, send mail


Now online: A description of SubtiWiki, SubtiPathways, and SubtInteract in the 2012 Database issue of Nucleic Acids Research

Ulrike Mäder, Arne G Schmeisky, Lope A Flórez, Jörg Stülke
SubtiWiki--a comprehensive community resource for the model organism Bacillus subtilis.
Nucleic Acids Res.: 2012, 40(Database issue);D1278-87
[PubMed:22096228] [WorldCat.org] [DOI] (I p)



A collection of important papers on B. subtilis metabolism can be found here


Carbon metabolism

Central carbon metabolism

Utilization of different carbon sources


Nitrogen and amino acid metabolism

Ammonium assimilation and glutamate metabolism (incl. glutamine and arginine)

Alanine, glycine, serine

Aspartate, asparagine

Cysteine, methionine

Histidine

Isoleucine, valine, leucine

Lysine, threonine

Phenylalanine, tyrosine, tryptophan

Proline

Utilization of other nitrogen sources


Lipid metabolism

Fatty acid and phospholipid biosynthesis

Fatty acid degradation


Nucleotides

Gene regulation of nucleotide metabolism

Nucleoside catabolism

Purine biosynthesis

Purine catabolism

Purine salvage pathways

Pyrimidine metabolism


Metabolism of cofactors

CoA synthesis

Folate biosynthesis

Menaquinone

Riboflavin and FAD synthesis

Thiamin synthesis

Biotin synthesis


Other pathways

Cell wall

Murein recycling

Stress responses

Phosphorelay

Sulfate assimilation

tRNA charging

Biofilm formation

Protein secretion

metal ion homeostasis

Publications describing SubtiWiki and SubtiPathways

Ulrike Mäder, Arne G Schmeisky, Lope A Flórez, Jörg Stülke
SubtiWiki--a comprehensive community resource for the model organism Bacillus subtilis.
Nucleic Acids Res.: 2012, 40(Database issue);D1278-87
[PubMed:22096228] [WorldCat.org] [DOI] (I p)

Christoph R Lammers, Lope A Flórez, Arne G Schmeisky, Sebastian F Roppel, Ulrike Mäder, Leendert Hamoen, Jörg Stülke
Connecting parts with processes: SubtiWiki and SubtiPathways integrate gene and pathway annotation for Bacillus subtilis.
Microbiology (Reading, Engl.): 2010, 156(Pt 3);849-59
[PubMed:19959575] [WorldCat.org] [DOI] (I p)