Difference between revisions of "SubtiPathways"
| Line 1: | Line 1: | ||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
[[File:Pathway_start_page_small.png|right|link=http://subtipathways.uni-goettingen.de/]] | [[File:Pathway_start_page_small.png|right|link=http://subtipathways.uni-goettingen.de/]] | ||
| − | [[File:Legende.jpg|250px|thumb|right|'''legend for ''Subti''Pathways | + | [[File:Legende.jpg|250px|thumb|right|'''legend for ''Subti''Pathways <br/>graphical notation: click to enlarge''']] |
| − | + | <big>'''''Subti''Pathways''' 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).<br/><br/>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 ''Subti''Wiki and PubChem pages, respectively. There is a short description for each protein in the bubbles, too.</big> | |
| − | + | <big>'''Contact:'''</big> [http://wwwuser.gwdg.de/~genmibio/stuelke.html General Microbiology, University of Göttingen], [mailto:jstuelk@gwdg.de send mail] | |
| − | + | <big>'''A publication describing ''Subti''Wiki and ''Subti''Pathways:'''</big> | |
| − | + | <pubmed>19959575 </pubmed> | |
__NOTOC__ | __NOTOC__ | ||
| − | + | <br/> | |
== A collection of important papers on ''B. subtilis'' [[metabolism]] can be found [[metabolism|here]] == | == A collection of important papers on ''B. subtilis'' [[metabolism]] can be found [[metabolism|here]] == | ||
| − | + | <br/> | |
== Carbon metabolism == | == Carbon metabolism == | ||
| Line 29: | Line 21: | ||
=== [http://subtiwiki.uni-goettingen.de/pathways/carbohydrate_metabolic_pathways.html Utilization of different carbon sources] === | === [http://subtiwiki.uni-goettingen.de/pathways/carbohydrate_metabolic_pathways.html Utilization of different carbon sources] === | ||
| − | + | <br/> | |
== Nitrogen and amino acid metabolism == | == Nitrogen and amino acid metabolism == | ||
| Line 52: | Line 44: | ||
=== [http://subtiwiki.uni-goettingen.de/pathways/other_nitrogen_sources/index.html Utilization of other nitrogen sources] === | === [http://subtiwiki.uni-goettingen.de/pathways/other_nitrogen_sources/index.html Utilization of other nitrogen sources] === | ||
| − | + | <br/> | |
== Lipid metabolism == | == Lipid metabolism == | ||
| Line 60: | Line 52: | ||
=== [http://subtiwiki.uni-goettingen.de/pathways/fatty_acid_degradation.html Fatty acid degradation] === | === [http://subtiwiki.uni-goettingen.de/pathways/fatty_acid_degradation.html Fatty acid degradation] === | ||
| − | + | <br/> | |
== Nucleotides == | == Nucleotides == | ||
| Line 76: | Line 68: | ||
=== [http://subtiwiki.uni-goettingen.de/pathways/pyrimidines_metabolism.html Pyrimidine metabolism] === | === [http://subtiwiki.uni-goettingen.de/pathways/pyrimidines_metabolism.html Pyrimidine metabolism] === | ||
| − | + | <br/> | |
== Metabolism of cofactors == | == Metabolism of cofactors == | ||
| Line 91: | Line 83: | ||
=== [http://subtiwiki.uni-goettingen.de/pathways/biotin/index.html Biotin synthesis] === | === [http://subtiwiki.uni-goettingen.de/pathways/biotin/index.html Biotin synthesis] === | ||
| − | + | <br/> | |
== Other pathways == | == Other pathways == | ||
Revision as of 06:08, 24 November 2010
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
A publication describing SubtiWiki and SubtiPathways:
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): 2010, 156(Pt 3);849-859
[PubMed:19959575]
[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
